Land formation seriously disturbs coastal salt marsh wetland ecosystems, while its influences on soil organic carbon (SOC) under chronosequences remain unclear. In this study, the impacts of the land formation time (from one to fourteen years) and soil properties on the chronosequences changes of SOC in the nascent wetland of Hengsha Island were investigated. The study results showed the following. (1) As the land-formation time extended, the SOC experienced a significant increase, tripling after a period of 14 years. The changes in SOC occurred mainly in the surface layer but not in the deep soil layer. Specifically, the surface layer’s average SOC reached 5.52 g·kg−1, markedly higher than 3.17 g·kg−1 in the deeper layer. (2) Spearman correlation analysis revealed that the ammonium nitrogen (NH4+-N), aboveground biomass (AGB), and soil water content (SWC) were positively correlated with the SOC. Methane emissions (CH4) and SOC exhibited a negative correlation. (3) The structural equation model (SEM) illustrated that the duration of soil deformation directly impacted the vegetation growth and affected the distribution characteristics of the SOC by modifying the soil environmental conditions. Changes in SOC following land formation influenced the rapid succession of soil properties and vegetation, with the modification of carbon sinks in the ecosystems.