Soil total organic carbon (TOC) and total nitrogen (TN) in estuarine areas show distinct heterogeneities in horizontal and vertical distributions due to complex influencing factors, and clarifying the horizontal and vertical distributions and their influencing factors is of great significance. In this study, the eastern Chongming Island in the Yangtze River estuary in China was selected as the study area, and the horizontal and vertical distributions of soil TOC and TN in different layers of 0–20 cm, 20–40 cm, and 40–60 cm were exhibited in maps and analyzed in different community types. Then, a total of 17 potential factors in aspects of soil, vegetation, atmosphere, landscape, and position were adopted and their single and synergistic effects on the spatial patterns of TOC and TN were identified from different perspectives. Results indicated that the mean values of TOC and TN in the entire study area decreased from surface to bottom layers. TOC and TN showed distinct spatial heterogeneities in different sampling sites and community types; they were generally high in the inner part and low in the alongshore areas in surface soils and showed opposite spatial characteristics in bottom soils; and woodland showed the highest TOC and TN in surface soils and the lowest values in bottom soils of different community types. TOC and TN in different layers, as well as the variations of TOC and TN across layers, exhibited specific and different spatial patterns under the complex factors. In soil factors, pH and available phosphorus showed the closest correlations with TOC and TN in different layers; in land surface factors, plant diversity and growth condition contributed the most to the horizontal distribution while plant growth condition and bare soil index exerted the highest influences on the vertical distribution.