Autophagy is a conserved, inherent cellular mechanism involving various proteins, which transports cytoplasmic material to the lysosome for degradation. It maintains cell homeostasis by ensuring the renewal of abnormal/senescent organelles and the circulation of nutrients. Autophagy is also an important intracellular defense mechanism. It blocks virus invasion by targeting viral particles or viral components for degradation. It can also promote the interaction of viral components with receptors in the innate immune pathway to stimulate the production of interferon, and even can utilize the autophagosome membrane or autophagosome for self-replication. In order to cope with such pressure, viruses have evolved various complex strategies to antagonize the antiviral effects of the autophagy. This review aims to summarize the role of autophagy in antiviral immunity and the specific mechanism of virus regulating autophagy. It also briefly introduces the research progress in autophagy-related diseases and therapeutic drugs.