The metamorphosis of flatfish is unique, especially its eye migration. Autophagy has been found to be involved in a variety of organisms' metamorphosis. In order to explore the relationship between autophagy and flatfish metamorphosis, we investigated the expression of autophagy marker gene lc3b during the metamorphosis using real-time quantitative polymerase chain reaction and in situ RNA hybridization. Besides, we inhibited cell division, which was reported as the force source of eye migration, and autophagy around the mobile eye by microinjecting the inhibitors to explore the effects on autophagy expression and eye migration. We found that autophagy taking place during the metamorphosis, particularly in the areas around the eyes. In addition, the eye migration could be blocked by inhibiting the autophagy in the supraorbital area of the blind side, and after we blocked the eye migration by inhibiting cell proliferation in the infraorbital area of the blind side, the autophagy around the eye was partially inhibited. These findings indicate that the autophagy around the eyes caused by eye migration. Moreover, the cell death caused by autophagy loosen the orbital tissue to create space for the eye migration.