Molecular hydrogen, as an effective anti-oxidative stress reagent, has been extensively studied in medicine with new developments continuing to be reported during the years. This review firstly discusses the mechanism of molecular hydrogen of alleviating oxidative stress. Considering the current antioxidant demand in clinical dental treatment, we summarize the progress and future potential of hydrogen's application in periodontitis. Finally, taking its treatment of periodontitis as an example, we develop an Essence-Necessity-Feasibility-Practice (ENFP) benefit evaluation model for whether to introduce new reagents in medical treatment and propose our conclusions on the application of molecular hydrogen before, during, and after periodontal surgeries.