The gut is the largest reservoir of human flora. In the last decade, with the increasing investigations on the relationships between gut microbiota and human health diseases, gut bacteriophage has also drawn more attention. However, the research of gut bacteriophage is still in its infancy, hampered by delayed progress in the experimental and bioinformatical technology for gut bacteriophage and virome. Thus, this review first summarizes the research methodology of gut bacteriophage in computation and experiments, including sequening analysis and phage isolation, etc. Then, phage taxonomy, phage-host interactions, and the clinical applications of gut bacteriophage are also discussed. Finally, this review looks forward to the challenges and opportunities for gut bacteriophage research in data and physical resources, bioinformatical and experimental technology, interactions with intestinal bacteria, interventions on human diseases, etc.