For a long time, intercropping and rotation of leguminous with non-leguminous crops is widely used to reduce the application of nitrogen fertilizer and increase yield in agroecosystems. At present, most researchers considered that this management measure is helpful for reducing fertilizer consumption and increasing its efficiency, as it can improve nutrient supply of legumestonon-legumes, the spatial nutrient utilization efficiency by enhancing soil spatial heterogeneity, and improve soil structure and disease resistance. However, current theories cannot fully explain the positive effect of crop rotation and inter-cropping systems involving legumes. A large amount of hydrogen (H2) can be produced as an obligatory by-product of nitrogenase responsible for nitrogen (N2) fixation in the root nodules of leguminous plants. Despite of substantial amounts of H2 enriched in the rhizosphere of legumes, only a minor proportion of H2 is found to leak to soil surface. Increasing evidence showed that most H2 released in soil is immediately depleted in the surrounding of N2-fixing nodules by H2-oxidizing bacteria (HOB) thriving in soil. HOB can use H2 as an electron donor to assimilate and fix CO2 through redox reactions to synthesize cellular substances and consequently promote plant growth. To date, however, little is known about the biological mechanism and ecological process behind the "hydrogen fertilizer effect". Therefore, we review the H2-induced plant growth-promoting effects and its microbiological mechanisms. Our aims were to explore a new way for enhancing agroecosystem production, and to provide scientific basis for future utilization of H2 in agricultural production practices.