As a vital issue of information based fisheries, morphological feature detection of fish is widely applied to many domains. The existing fish eye feature detection mainly depends on manual work, and the operation process is complex with low efficiency and subjective results. Therefore, a detection method of fish eye based on image processing and least square ellipse fitting is proposed. Firstly, fish images are collected from facilities in farm. Then image preprocessing is performed on fish eye pupil and iris. Finally, the edge of the fish eye pupil and iris is identified by ellipse fitting method. As seen from the results, pupil detection costs an average time of 325.96ms, iris detection costs an average time of 364.57ms, pupil detection error is 7.247 (11.82%) mm, and iris detection error is 12.179 (14.05%) mm. Studies have shown that the proposed method can not only solve the problem that manual work is complex and subjective, but also avoid the time-consuming measuring process and provide a new way for large quantities of fish eye non-contact measurement.