Salt marsh wetlands are regarded as important blue carbon ecosystems, which play important roles in mitigating the greenhouse effects and resist global climate change. Organic carbon stored in the soil (soil organic carbon, SOC) is the main component of the carbon sink in salt marsh wetlands, but its storage is susceptible to various environmental factors. The changes of environment factors, such as vegetation coverage and soil physicochemical factors, could significantly affect the SOC storage capacity of salt marsh wetlands and change the spatial distribution of soil carbon storage, especially in estuarine area where there are obvious spatial and temporal differences in environment. Based on the salt marsh wetlands around the Chongming Island in the Yangtze Estuary as a typical study area, the SOC content of different line transects and different vegetation types along the elevation change from sea to land were measured around the island, and the physicochemical properties of plants and soil (salinity, bulk density, C/N ratio, etc.) at each sampling point were monitored simultaneously. Besides, the spatial distribution pattern of SOC storage in the salt marsh wetland around the Chongming Island and its influencing factors were analyzed. The results showed that: (1) there was significantly spatial heterogeneity in the SOC content and storage in the salt marsh wetland around the Chongming Island, with higher SOC content on the north side and higher SOC storage on the northeast side. (2) on the vertical soil layers, the SOC content showed a decreasing trend with the increase of soil depth, and the SOC storage per unit area at 0-50 cm depth was higher than that at 50-100 cm depth. (3) plant types and soil physicochemical factors (soil C/N, soil salinity, soil bulk density, etc.) regulated and interacted with each other, which affected the spatial pattern of the SOC storage in the salt marsh wetlands around the Chongming Island to some extent. Studies have shown that, due to the spatial heterogeneity of vegetation types and soil physicochemical properties in estuaries, the SOC storage patterns in salt marsh wetlands were also prone to spatial variation. Therefore, the spatial heterogeneity of the environment and ecology between regions should be fully considered when carrying out the investigation of carbon storage, which not only helps to scientifically evaluate the carbon storage capacity of salt marshes, but also will be of great significance to further explore the carbon storage mechanism of salt marshes and implement the carbon sequestration and sink increase of blue carbon in the salt marshes.