Autophagy, a cellular housekeeping process, is indispensable to controlling the homeostasis of cytoplasm by removing unused proteins and damaged cell organelles. This process involves different types of human diseases, including cancers, neurodegenerative diseases and infectious diseases. Neurodegeneration is a critical pathological process of many eye diseases, such as glaucoma and age-related macular degeneration. The retina and all intraocular cells are constantly exposed to environmental stress and injuries, including oxidative stress and starvation, which lead to autophagy. Autophagy promotes cell survival through the recycling of metabolic precursors, or promotes cell death if autophagy is over-active. Additionally, autophagy and apoptosis have been shown to be harmonious or contrasting, depending on different experimental contexts. All of this contributes to the pathogenesis of many diseases. This paper reviews the mechanisms and regulation involved in autophagy, current understandings of neuronal autophagy in glaucoma and retina and strategies for therapeutic modulation.