Purpose <p>Research on the coupling effect between soil and plants, as well as its impact on soil organic carbon (SOC) components, is instrumental in elucidating the mechanisms that maintain the stability of carbon pools in inland salt marsh wetlands.</p> Materials and methods <p>In the inland salt marsh wetland of Sugan Lake, three waterlogging gradient plots (I, II and III) were established sequentially from the lake shore, aligned perpendicularly to the shoreline based on historical water level data. Utilizing community investigations and structural equation modeling, this study examined the spatial distribution of SOC components and the stability of the carbon pool across varying waterlogging gradients.</p> Results and analysis <p>As waterlogging duration decreased, recalcitrant (ROC) and labile organic carbon (LOC) increased horizontally in each soil layer, with vertical differences. LOC correlated positively with underground biomass, clay, total dissolved solids, and total nitrogen (<i>P</i> &lt; 0.01); ROC correlated with clay and salinity (<i>P</i> &lt; 0.01). Soil properties were the primary direct driver of carbon stability (0.214), while plant characteristics directly (0.145) and indirectly (0.523) enhanced stability via soil properties.</p> Conclusions <p>Eco-hydrological processes influence soil physicochemical properties and plant community structure in inland salt marshes. They alter the spatial distribution and mass fraction of SOC components, thereby affecting the carbon pool stability in these wetland ecosystems. This understanding can serve as a reference for the precise assessment of SOC in wetland ecosystems and for the management of soil carbon pools.</p>