AbstractCoastal mangrove wetlands experience unique land‐sea interaction including periodic tidal and sea breeze activity; however, their impacts on mangrove net ecosystem exchange (NEE) of carbon dioxide have not been well investigated. In this regard, continuous eddy covariance and auxiliary measurements were conducted to characterize the temporal variations in NEE and environmental controls in a subtropical mangrove of southeastern China. Over a 3‐year measurement period, this mangrove acted a consistent carbon sink showing weak seasonality in NEE with a stronger sink in spring. Environmental controls on NEE varied across time scales: (1) at half‐hourly time scale especially for summer and autumn, high temperature and vapor pressure deficit (VPD) suppressed daytime carbon uptake, while inundation fraction and rain restrained nighttime carbon efflux; (2) the importance of environmental impacts on daily NEE decreased in the order of photosynthetically active radiation, air temperature, sea breeze, VPD, tidal salinity, and inundation; (3) monthly carbon uptake was statistically negatively and positively correlated with inundation fraction and rain, respectively. Periodic tidal inundation exerted both direct and indirect effects, but their relative importance changed across time scales. Cooling and wetting effects from regular sea breeze relieved atmospheric temperature/moisture stresses at afternoon, acting as an important indirect effect to promote carbon uptake. This study confirms the importance of previously neglected indirect effects of land‐sea interaction of tidal and sea breeze activity on mangrove NEE.