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.