It is more correct to call this species the Blakiston's eagle owl. This is because it is more closely related to the Eurasian eagle-owl by studies of the main subgenus of the species, B. b. dumeril, than to the subgenus of fish owls that it was believed to be more close to, i.e. Ketupu. This was proven by osteological (skeleton/bone-related) and DNA-based tests in 2003 by ornithologists/taxonomists Michael Wink and Claus König, author of Owls of the World. However, the other fish owls are not believed to be divergent enough to support a separate genus either and now all fish owls are generally also included in the Bubo genus. Given that it shares genetic material osteological characteristics with the eagle-owl and also seems to share some characteristics with the other three fish owls (especially the brown species), the place of the Blakiston's fish owls in this evolutionary chain is ambiguous. Some authors have wondered whether the Blakiston's represents an intermediate step between traditional eagle-owls and the other fish owls, despite the current gap in distribution between Blakiston's and other fish owls. Whether other Asian eagle-owls with sideways slanting ear-tufts, namely the spot-bellied (B. nipalensis), the barred (B. sumatranus) and especially the somewhat superficially fish owl-like dusky eagle-owl (B. coromandus) are closely related to the fish owls and/or the Blakiston's is also unclear. Despite a few authors also include them in Bubo, the fishing owls of Africa, generally classified in the genus Scotopelia, seem to be unrelated in every major way, based on external characteristics, oseology and preliminary genetic materials, to the fish owls and it is unclear how, and if, they are related to typical eagle-owls.
Blakiston's fish owl is the largest living species of owl. A pair field study of the species showed males weighing from 2.95 to 3.6 kg (6.5 to 7.9 lb), while the female, at up to 2.95 to 4.6 kg (6.5 to 10.1 lb), is about 25% larger. Around February, the average weight of Russian fish owls was 3.1 kg (6.8 lb) in males and 3.25 kg (7.2 lb) in females, typically when their body mass at its lowest throughout the year. Blakiston's fish owl measures 60 to 72 cm (24 to 28 in) in total length, and thus measures slightly less at average and maximum length than the great gray owl (Strix nebulosa), a species which has a significantly lower body mass. The Eurasian eagle-owl (B. bubo) is sometimes considered the largest overall living owl species. The three largest races of eagle-owl, all found in Siberia and the Russian Far East, are close in size to the Blakiston's fish owl. According to Heimo Mikkola, the very largest specimen of eagle-owl was 30 mm (1.2 in) longer in bill-to-tail length than the longest Blakiston's fish owl, while the top weight of the two species is exactly the same. The longest great gray owl was 120 mm (4.7 in) longer than the biggest Blakiston's fish owl but would be about 2.5 times lighter than the weight of the largest female Blakiston's. However, the average measurements of Blakiston's fish owl surpass the average measurements of the Eurasian eagle-owl in the three major categories: weight, length, and wingspan, making Blakiston's the overall largest species of owl. Even the large Siberian races of eagle-owl are slightly smaller on average than the Blakiston's, at least in terms of body mass and wing size. The maximum wingspan of the Blakiston's fish owl is also greater than any known eagle-owl. The wingspan range known for Blakiston's fish owls is 178 to 190 cm (5 ft 10 in to 6 ft 3 in). It is possible the largest specimens can attain a wingspan of approximately 200 cm (6 ft 7 in). The Blakiston's is noticeably larger than the other three extant species of fish owl.
In terms of structure, the Blakiston's fish owl is more similar to eagle-owls than it is to other fish owls but it shares a few characteristics with both types of owl. Like all fish owls, its bill is relatively long, the body relatively husky and wings are relatively long compared to eagle-owls. It also shares with other fish owls a comparatively long tarsi, although relative to their size the three smaller fish owl have a proportionately longer tarsus. Other than these few characteristics, a Blakiston's fish owl skull and skeleton is practically the same as that of a Eurasian eagle-owl. The talons of the Blakiston's fish owl are similar in shape and size to those of the Eurasian eagle-owls. It has been stated that the combination of wavy cross patterns on the underside of the Blakiston's plumage and its huge talons make it look strikingly like an outsized great horned owl (B. virginianus) from below. Two external characteristics that Blakiston's share with eagle-owls, but not with the other fish owls, is that its tarsi are totally feathered and that its wing beats are silent, although apparently the Blakiston's has relatively fewer sound-blocking combs on its wing primaries than the a comparable eagle-owl would. Among standard measurements, which at average and maximum are greater than any other living owl other than tail length, the wing chord measures 447–560 mm (17.6–22.0 in), the tail measures 243–305 mm (9.6–12.0 in), the tarsus is 73–102 mm (2.9–4.0 in) and the culmen is around 55 to 71 mm (2.2 to 2.8 in).
Superficially, this owl somewhat resembles the Eurasian eagle-owl but is paler and has relatively broad and ragged ear tufts which hang slightly to the side. The upperparts are buff-brown and heavily streaked with darker brown coloration. The underparts are a paler buffish brown and less heavily streaked. The throat is white. The iris is yellow (whereas the Eurasian eagle-owl typically has an orange iris). The Eurasian eagle-owl and Blakiston's fish owl both occur in the Russian Far East and are potentially could compete for resources, although no scientifically observed interactions of any kind have been reported between these two largest owl species. It is likely, given the sizeable gap between the dietary preferences of the species (mainly aquatic animals in the Blakiston's, mainly upland, terrestrial species in the eagle-owl) that competition for food is not normally a serious problem. Identification of the Blakiston's from other fish owls is not an issue as there is a gap of distribution of approximately 800 km (500 mi) between the ranges of the Blakiston's and the tawny fish owl (B. flavipes) and about 2,000 km (1,200 mi) separates the range of the Blakiston's and the brown fish owl (B. zeylonensis). Improbably, early naturalist thought that the Blakiston's and brown fish owls belonged to the same species. The streaking on the underside of the Brown and Blakiston's are similar and their songs sound more similar to each other than they do with the two songs of the other two species of fish owl.
Vocalizations differ among the recognized subspecies. In the nominate subspecies from Japan, the male calls twice and the female responds with one note, whereas the mainland subspecies has a somewhat more elaborate, four-note duet: HOO-hoo, HOOO-hoooo (here, the male call is in capital letters (HOO) and the female call in lower case (hoo)). The transliterations of the calls of owls from Russia, representative of the owl's vocal variations, are SHOO-boo and FOO-foo-foo. The territorial song or call in Russia in particular has been described as somewhat like a short, deep eagle-owl's call. Despite its slightly larger size, the Blakiston's fish owls voice is not as sonorous or as far-carrying as is the Eurasian eagle-owl's voice is. As in most owls, vocal activity tends to peak directly before nesting activity begins, so peaks around February in this species. This duet of pairs of Blakiston's fish owl in the period leading up the breeding season is so synchronized that those unfamiliar with the call often think it is only one bird calling. When an individual bird calls, it may sound like hoo-hooo. Juveniles have a characteristic shriek, typically a startling and slurred phee-phee-phee.