He brought out a second and enlarged edition of the Hortus Kewensis in 1810–1813, a catalogue of the plants at Kew Gardens, the first edition of which was written by his father William Aiton. Aiton succeeded his father as director at Kew Gardens in 1793 and was commissioned by George IV to lay out the gardens at the Royal Brighton Pavilion and at Buckingham Palace Gardens.
Aiton was one of the founders and an active fellow of the Royal Horticultural Society.
He retired in 1841 but remained living at Kew, although passing much of his time with his brother at Kensington where he died on 9 October 1849. He is buried at Kew.