With the worldwide spread of antimicrobial-resistant bacteria, phage therapy has attracted renewed attention as an effective alternative to antibiotics. On the other hand, with the development of research on the interactions between human microbiota and the host, a number of studies have focused on regulating the microbiota to affect human health. The use of phages to reduce the abundance of characteristic bacteria positively associated with disease progression has become a more precise prevention or adjuvant treatment strategy for non-infectious diseases such as cancer, alcoholic liver disease and diabetes. In this paper, the progress of phage therapy applications in infectious and non-infectious diseases was reviewed.