Molecular hydrogen is a key intermediary in the metabolic interactions of a wide variety of microorganisms. The activities of hydrogen-producing and hydrogen-consuming microorganisms in the environment determine the global hydrogen cycle, which has a potential driving effect on the biogeochemical cycle of other important elements. Environmental functional microorganisms play an important role in maintaining the balance of ecosystems and eliminating secondary pollution. Therefore, understanding the impact of hydrogen metabolizing (production and consumption of hydrogen) microorganisms on the ecological environment and its role and function in environmental bioremediation has vital significance and practical value for understanding the ecological and environmental effects of hydrogen and its application to bioremediation. This paper systematically analyzed the hydrogen metabolism process and the classification and function of hydrogenase, summarized the various ways of hydrogen production and consumption by microorganisms and their effects on soil ecological environment and bioremediation. The scientific and technical challenges existing in current hydrogen metabolism processes and the application of hydrogenase in environmental bioremediation were summarized. Besides, it was also proposed research ideas and key directions in this field to promote hydrogen as a bioenergy since it has become a promising strategy for environmental pollution remediation.