Coastal wetlands are of great importance for global carbon cycle and climate mitigation because of their strong carbon uptake capacity. However, the national-scale ecosystem carbon exchange dynamics in coastal wetlands, including magnitudes, spatial patterns, and controlling mechanisms, remains poorly understood. In this study, we utilized eddy covariance measurements from China's coastal wetlands to quantify carbon fluxes, assess their spatial patterns, and explore the controlling mechanisms. Integrating climate, vegetation, and soil factors, we constructed a cascaded relationship network to reveal the potential controlling mechanisms of spatial variations in carbon fluxes. The results revealed that gross primary production (GPP) and ecosystem respiration (ER) were 1405 ± 656 (mean ± sd) gC m−2 yr−1and 893 ± 465, respectively. Net ecosystem production (NEP) in coastal wetlands (567 ± 348 gC m−2 yr−1) exceeded China's terrestrial and marine ecosystems by 2–8 times, highlighting their significant carbon sink capacity. The carbon sink capacity in mangroves was significantly higher than salt marsh, exhibiting a twofold difference in NEP. Spatially, carbon fluxes displayed negative correlations with latitude, indicating the influence of climate features. Although tropical climate zone exhibited significantly higher carbon fluxes than temperate zone, no differences were observed between subtropics zone with others due to the distribution of mixed plants and largest area. The structural equation model (SEM) showed that the climate factors, including temperature, precipitation, and net radiation indirectly promoted GPP and ER through regulating the physiological process of mangrove and salt marsh, as well as soil carbon production and consumption. The cascaded relationship of climate-vegetation-soil showed in SEM explained 71–85 % of the spatial variations in GPP and ER, and ultimately accounted for 85 % of NEP. The carbon consumption efficiency (ER/GPP) in coastal vegetations was of 0.6, lower than that of global and China's terrestrial ecosystems, suggesting their strong efficiency in carbon fixation in coastal wetlands. Lastly, the scenario simulation results implied the importance of coastal vegetation restoration on enhancing blue carbon benefits.