In the past few decades, a large number of pesticides have been widely used for plant protection. Pesticides may enter non-target organisms through multiple ways and bring potential health risks. There is a dense and diverse microbial community in the intestines of mammals, which is called the gut microbiota. The gut microbiota and its metabolites play vital roles in maintaining the health of the host. Interestingly, many studies have shown that exposure to multiple pesticides could affect the gut microbiota of the host. However, the roles of gut microbiota and its related metabolites in the host health effects induced by pesticide exposure of non-target organisms need further study. We reviewed the relationships between pesticide exposure and host health effects as well as between the gut microbiota and host health effects. Importantly, we reviewed the latest research on the gut microbiota and its metabolites in the host health effects induced by pesticide exposure.