As a well-known biological vertebrate model, zebrafish is an ideal object to study pathogen infection and immunity. Many bacteria-zebrafish infection models have been constructed successfully. On its translucent larval stage, only innate immune system has developed perfectly. So using zebrafish to study innate immunity has many advantages and can avoid the interference of adaptive immunity. As a highly conservative intracellular degradation process, autophagy is an important event of innate immunity. It can initiate a response against bacteria through Toll-like receptors or mucosal immune system. A preliminary study on autophagy of zebrafish associated with its development and eliminating maternal residues has been going on. And now a new bacteria-zebrafish model for studying autophagy has been constructed successfully, which is of great significance to research the mechanisms of xenophagy. Here we summarize the results gained from zebrafish on pathogen infection and immunity as well as autophagy in recent years.