Wetland CH₄ emissions are among the most uncertain components of the global CH₄ budget. The complex nature of wetland CH₄ processes makes it challenging to identify causal relationships for improving our understanding and predictability of CH₄ emissions. In this study, we used the flux measurements of CH₄ from eddy covariance towers (30 sites from 4 wetlands types: bog, fen, marsh, and wet tundra) to construct a causality-constrained machine learning (ML) framework to explain the regulative factors and to capture CH₄ emissions at sub-seasonal scale. We found that soil temperature is the dominant factor for CH₄ emissions in all studied wetland types. Ecosystem respiration (CO₂) and gross primary productivity exert controls at bog, fen, and marsh sites with lagged responses of days to weeks. Integrating these asynchronous environmental and biological causal relationships in predictive models significantly improved model performance. More importantly, modeled CH₄ emissions differed by up to a factor of 4 under a +1°C warming scenario when causality constraints were considered. These results highlight the significant role of causality in modeling wetland CH₄ emissions especially under future warming conditions, while traditional data-driven ML models may reproduce observations for the wrong reasons. Our proposed causality-guided model could benefit predictive modeling, large-scale upscaling, data gap-filling, and surrogate modeling of wetland CH₄ emissions within earth system land models.