The invention belongs to the technical field of fish cultivation and relates to an automatic sorting device for female and male fries of Cynoglossus semilaevis and an application method thereof. The automatic sorting device for female and male fries of Cynoglossus semilaevis comprises rollers, supports, a light source control switch, a light source fixing table, a light source, an identifying platform, a fish incoming channel, an identifying channel, a retaining plate, a water inlet for the fish incoming channel, an image information acquisition and processing system, a wireless remote control, an automatic control device, a fish outgoing channel, a male fry outlet, a female fry sorting retainer, a female fry sorting retainer, and a female fry outlet. The automatic sorting device for female and male fries of Cynoglossus semilaevis allows female and male fries to be distinguished in the early farming stage of Cynoglossus semilaevis, never causes physiological stress or body surface injury to the fry, and provides increased accuracy of distinguishing female and male fries and increased survival rate. In addition, with the integration of the technical design of modern information equipment, the automatic sorting device can provide automatic distinguishing and sorting for female and male fries, female and male fries are screened more efficiently, manpower and material resources are saved greatly, and farming benefit is improved.