Oral diseases can affect the quality of life of patients and cause secondary systemic diseases, thereby harming systemic health. Hydrogen has been shown to exhibit anti-oxidant stress, anti-inflammatory and anti-apoptosis and other effects, indicating its therapeutic significance for many kinds of diseases. Hydrogen administered through different methods can effectively reduce plaque biofilm formation, resist oxidative stress, inhibit the inflammatory response, and promote tissue repair and regeneration. This review summarizes the primary strategies for and research on hydrogen therapy, as well as the application of hydrogen in oral diseases such as dental caries, periodontitis, peri-implantitis, oral mucosal diseases, jaw diseases, oral and maxillofacial tumors, and trigeminal neuralgia. We highlight the regulatory effects of hydrogen on the functional states and interactions of common oral disease pathogens and various cells, including immune cells, osteoblast-associated cells, osteoclasts, and fibroblasts, and summarize the involved signaling pathways. In addition, this paper discusses the problems and shortcomings of the existing research, and highlights the directions for future development to provide the basis and support for future investigations into the mechanisms through which hydrogen exerts antioxidant stress and anti-inflammatory activity, promotes mucosal healing, enhances bone regeneration, as well as alleviates neuropathic pain.