Methane (CH₄) emissions from terrestrial systems are posited to increase, which can offset mitigation efforts and accelerate climate change. Yet, the accuracy of modeled CH₄ emissions is sensitive to the prescribed CH₄ production (or emission) temperature dependencies that are currently uncertain. Here, we estimated the temperature dependence of CH₄ emission using data collected by the recent FLUXNET-CH₄ synthesis. Our results indicate that CH₄ emissions are hysteretic to air and soil temperatures, which challenges the view of a unified static temperature dependence for CH₄ emissions across different ecosystems. We found that a proper representation of spatial heterogeneity and temporal variability is critical to a reliable CH₄ emission parameterization. For example, the R² values for CH₄ emission predictions improve from 0 to 0.29 (using a unified temperature dependence model across all sites and all years) to 0.37 to 0.76 (using site-year specific temperature dependence models) at the eight examined ecosystems. Our model simulations demonstrate that CH₄ emission hysteresis stems from substrate-mediated microbial responses to temperature that stimulate greater CH₄ emissions later in the thawed season. Collectively, our findings show that CH₄ emissions predicted by many existing terrestrial biogeochemical models may be biased by -21 to 81% due to improper representation of microbial and abiotic interactions. We acknowledge the FLUXNET-CH₄ contributors for the data provided in these analyses.