The invention discloses a fish skin separation method based on three-dimensional scanning, which is based on a fish skin separation device. The fish skin separation device comprises a holding mechanism, a circular cutting knife (1), a separation knife (2) and a skin-stripping mechanism (3). The holding mechanism comprises a gill hook (4) and a tail clamp mechanism (5). The circular cutting knife is arranged at an eccentric position of a central axial line between the gill hook and the tail clamp mechanism. The separation knife and the skin-stripping mechanism are arranged at the side of the gill hook. The fish skin separation method includes the steps of scanning fish body through a three-dimensional image to obtain circular cutting position and path, separation path, longitudinal cutting path and stripping path; holding the to-be-skinned fish body in a horizontal manner front-and-back by the holding mechanism, circularly cutting the fish body around the fish body through the circular cutting knife; separating fish skin from fish body by the separation knife being stretched into the fish body from cut marks at the circularly cut position; longitudinally cutting the fish skin in the length direction of the fish body by means of the circular cutting knife; and finally removing the fish skin by the skin-stripping mechanism. The fish skin separation method achieves automatic separation of the fish skin, increases stripping efficiency of the fish skin and avoids damage on the fish skin.