Gut microbiota affects human nutrition, metabolism, immune development and functionality, and other physiological activities. Recent findings have revealed the roles of gut microbiota in susceptibility and prognosis in virus infection diseases. Here, we summarize the relationship, interaction between gut microbiota and enteric virus infection diseases, as well as non-enteric virus infection diseases. In addition, the potential therapies for modulating microbiota to prevent or treat virus infection diseases are discussed. This review will provide new ideas for further related research on prevention and control of virus infection diseases.