Methane (CH4) possesses a notably higher warming potential than carbon dioxide despite its lower atmospheric concentration, making it integral to global climate dynamics. Wetlands stand out as the predominant natural contributor to global methane emissions. Accurate modeling of methane emissions from wetlands is crucial for understanding and predicting climate change dynamics. However, such modeling efforts are often constrained by the inherent uncertainties in model parameters. Our work leverages machine learning (ML) to calibrate five physical parameters of the Energy Exascale Earth System Model (E3SM) land model (ELM) to improve the model’s accuracy in simulating wetland methane emissions. Unlike traditional deterministic calibration methods that target a single set of optimal values for each parameter, Bayesian calibration takes a probabilistic approach and enables capturing the inherent uncertainties in complex systems and providing robust parameter distributions for reliable predictions. However, Bayesian calibration requires numerous model runs and makes it computationally expensive. We employed an ML algorithm, Gaussian process regression (GPR), to emulate the ELM’s methane model, which dramatically reduced the computational time from 6 CPU hours to just 0.72 milliseconds per simulation. We exemplified the procedure at a representative FLUXNET-CH4 site (US-PFa) with the longest continuous methane emission data. Results showed that the default values for two of the five parameters examined were not aligned well with their respective posterior distributions, suggesting that the model’s default parameter values might not always be optimal for all sites, and that site-specific analysis is warranted. In particular, analyses at sites with different vegetation types and wetland characteristics could reveal more useful insights for understanding methane emissions modeling.