Wetlands account for up to 70% of the natural source of methane (CH4) in terrestrial ecosystems on a global scale. Soil microbes are the ultimate producers and biological consumers of CH4 in wetlands. Therefore, simulating microbial mechanisms of CH4 production and consumptionwould improve the predictability of CH4 flux in wetland ecosystems. In this study, we applied a microbial-explicit model, the CLM-Microbe, to simulate CH4 flux in three major natural wetlands in northeastern China. The CLM-Microbe model was able to capture the seasonal variation of gross primary productivity (GPP), dissolved organic carbon (DOC), and CH4 flux. The CLM-Microbe model explained more than 40% of the variation in GPP and CH4 flux across sites. Marsh wetlands had higher CH4 flux than mountain peatlands. Ebullition dominated the CH4 transport pathway in all three wetlands. The methanogenesis dominates while methanotroph makes a minor contribution to the CH4 flux, making all wetlands a CH4 source. Sensitivity analysis indicated that microbial growth and death rates are the key factors governing CH4 emission and vegetation physiological properties (flnr) and maintenance respiration predominate GPP variation. Explicitly simulating microbial processes allows genomic information to be incorporated, laying a foundation for better predicting CH4 dynamics under the changing environment.