Mitophagy is a selective autophagy refers to the autophagy process by which cells selectively remove mitochondria. Mitophagy plays important roles in clearing up dysfunctional mitochondria, reducing mitochondrial numbers and maintaining cell homeostasis. Its molecular mechanisms involve several proteins such as PINK1/Parkin, BNIP3, NIX, and FUNDC1. Mitochondrial dysfunction or damage may cause serious consequences, and may even lead to cell death. Studies have shown that disfunction of mitophagy is related to many eye diseases, for instance, cataract, glaucoma, age-related macular degeneration, diabetic retinopathy, etc. This review deals with the mechanisms of mitophagy and its research on ocular diseases.