Lakes are important sentinels of climate change and may contribute over 30% of natural methane (CH4) emissions; however, no earth system model (ESM) has represented lake CH4 dynamics. To fill this gap, we refined a process‐based lake biogeochemical model to simulate global lake CH4 emissions, including representation of lake bathymetry, oxic methane production (OMP), the effect of water level on ebullition, new non‐linear CH4 oxidation kinetics, and the coupling of sediment carbon pools with in‐lake primary production and terrigenous carbon loadings. We compiled a lake CH4 data set for model validation. The model shows promising performance in capturing the seasonal and inter‐annual variabilities of CH4 emissions at 10 representative lakes for different lake types and the variations in mean annual CH4 emissions among 106 lakes across the globe. The model reproduces the variations of the observed surface CH4 diffusion and ebullition along the gradients of lake latitude, depth, and surface area. The results suggest that OMP could play an important role in surface CH4 diffusion, and its relative importance is higher in less productive and/or deeper lakes. The model performance is improved for capturing CH4 outgassing events in non‐floodplain lakes and the seasonal variability of CH4 ebullition in floodplain lakes by representing the effect of water level on ebullition. The model can be integrated into ESMs to constrain global lake CH4 emissions and climate‐CH4 feedback.