The large uncertainties in estimating CH4 emissions from wetland ecosystems, the leading natural source to the atmosphere, substantially hinder the quantification of the global CH4 budget. This study used the IBIS-CH4 (Integrated BIosphere Simulator-Methane) model, a process-based model integrating microbial mechanisms associated with CH4 production and oxidation processes, to simulate global wetland CH4 emissions from 2001 to 2020. Initially, we employed the IBIS-CH4 model to evaluate its performance across 26 diverse wetland sites worldwide. The results showed that the magnitude and seasonality of observed CH4 fluxes over various wetland sites were well reproduced. We then used this model to estimate the annual global wetland CH4 emissions from 2001 to 2020, averaging 152.67 Tg CH4 yr−1, with a range of 135.72–167.57 Tg CH4 yr−1. The estimated global wetland CH4 emissions are generally in agreement with the current bottom-up estimates (117–256 Tg CH4 yr−1) and closely overlap with independent top-down estimates (139–183 Tg CH4 yr−1). During 2001–2020, the estimated global wetland CH4 emissions initially showed an increasing trend, followed by a decline. The peak of CH4 emissions reached in 2010, coinciding with the peak of wetland area. The majority of global wetland CH4 emissions were concentrated in tropical regions, which exhibited a clear seasonality and had a peak in July. The impact of meteorological factors on wetland CH4 emissions was greater than that of leaf area index, indicating the importance of soil hydrothermal conditions on wetland CH4 emissions.