Pearsonothuria graeffei is a roughly cylindrical, thin-walled sea cucumber that grows to about 30 centimetres (12 in) in length. Its mouth, at one end, is surrounded by a ring of up to 24 leaf-like, paddle-shaped tentacles with black stalks which are black on the upper side and white beneath. The anus is at the other end of the body and there are several rows of tube feet along the underside. The colour of the adults is pale brown and white, with black speckles and small thorn-like protuberances.
By contrast, the juveniles are brightly coloured, being white and blue or black, with a few large, yellow, thorn-like projections. This colouration makes them closely resemble the sea slug, Phyllidia varicosa, the bright colours of which warn predators of its toxicity. The appearance of the juvenile sea cucumbers begins to change when they grow larger than the slug and the mimicry is no longer effective.