Soil samplings and field monitoring were conducted to investigate CO2 fluxes properties on the interface of soil-atmosphere on intertidal zones to the north of the Yangtze Estuary. The net CO2 flux values indicated that the mud flat performed generally as a carbon sink. The low tidal flat (point III) was observed having the greatest CO2 flux where the higher Chl-a content brought stronger CO2 sequestration, and the lower TOC content led to less CO2 release in the processes of soil respiration and mineralization. In addition, groundwater level was studied as another critical factor of carbon cycle which had negatively correlated with CO2 net fluxes. The results provide a better understanding on restoring and protecting coastal wetlands and present an important opportunity for mitigating greenhouse gas emissions.