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The role of coastal mangrove wetlands in sequestering atmospheric carbon dioxide has been increasingly investigated in recent years. While studies have shown that mangroves are weak sources of methane (CH₄) emissions, measurements of CH₄ fluxes from these ecosystems remain scarce. In this study, we examined the temporal variation and biophysical drivers of ecosystem-scale CH₄ fluxes in China’s northernmost mangrove ecosystem based on eddy covariance measurements obtained over a 3-year period. In this mangrove, the annual CH₄ emissions ranged from 6.15 to 9.07 g C m⁻² year⁻¹. The daily CH₄ flux reached a peak of over 0.07 g C m⁻² day⁻¹ during the summer, while the winter CH₄ flux was negligible. Latent heat, soil temperature, photosynthetically active radiation, and tide water level were the primary factors controlling CH₄ emissions. This study not only elucidates the mechanisms influencing CH₄ emissions from mangroves, strengthening the understanding of these processes but also provides a valuable benchmark dataset to validate the model-derived carbon budget estimates for these ecosystems.