Autophagy, a highly conserved cellular metabolic process, serves as a vital mechanism for maintaining cellular homeostasis by forming autophagosomes to encapsulate and degrade damaged organelles, misfolded proteins, and invaded pathogens within cells. Although autophagy research has primarily focused on cancer and neurodegenerative diseases, growing evidence in recent years highlights its significant role in various infectious diseases (such as tuberculosis and fungal keratitis, etc). This review summarizes the molecular mechanisms of autophagy and its dynamic interplay with pathogen during infections, aiming to provide new insights for the prevention and treatment of infectious diseases.