Characteristics and tidal flat trends of soil organic matter (SOM) turnover were studied for the Chongmingdongtan Salt Marsh in the Yangtze River estuary, based on analyses of stable carbon isotope composition (δ13C), grain sizes and contents of particulate organic carbon (POC), total nitrogen (TN) and inorganic carbon (TIC) for three cores excavated from high tidal flat, middle tidal flat and bare flat. Results demonstrate that correlations between soil POC contents and δ13C values of the salt marsh cores were similar to those between soil organic carbon (SOC) contents and δ13C values of the upper soil layers of mountainous soil profiles with different altitudes. SOM of salt marsh was generally younger than 100 years, and originated mainly from topsoil erosions in catchments of the Yangtze River. Correlations of TN content with C/N ratio, POC content with TIC content and POC content with δ13C values for the cores suggest that turnover degrees of SOM from the salt marsh are overall low, and trends of SOM turnover are clear from the bare flat to the high tidal flat. Bare flat samples show characteristics of original sediments, with minor SOM turnover.Turnover processes of SOM have occurred and are discernable in the high and middle tidal flats, and the mixing degrees of SOM compartments with different turnover rates increase with evolution of the muddy tidal flat. The exclusive strata structure of alternate muddy laminae and silty laminae originated from dynamic depositional processes on muddy tidal flat was a great obstacle to vertical migration of dissolved materials, and SOM turnover was then constrained. The muddy tidal flat processes exerted direct influences on sequestration and turnover of SOM in the salt marsh, and had great constraints on the spatial and temporal characteristics of SOM turnover of the Chongmingdongtan Salt Marsh in the Yangtze River estuary.