Large-scale assessment of sedimentary organic carbon (SOC) storage in blue carbon ecosystems provides valuable benchmarks, yet averaging over regional heterogeneity in data synthesis can bias upscaling. To better understand the regional heterogeneity in SOC distribution and its controls across different coastal wetland types in subtropical China, Shenzhen was selected as a regional model with four coastal wetland types classified by geomorphology: coastal mangrove, semi-enclosed mangrove, spotted mangrove, and tidal flats. The results showed distinct contents and distribution patterns in soil texture, bulk organic carbon properties, and the lignin-phenol organic biomarker across wetland types. Varied organic carbon sources primarily controlled SOC in coastal mangrove sediments, but soil texture became the primary factor in spotted mangrove and tidal flat sediments. In semi-enclosed mangrove, sources, vegetation, and soil texture jointly affected SOC characteristics. The SOC storage in mangrove ecosystems was reassessed at 28.0 Gg C, which is 1.5-2 times the previous estimates. The SOC storage in tidal flats was first assessed at 4.7 Gg C. The spatial heterogeneity underscores the importance of regionally balanced data when upscaling to large-scale assessment, especially given the geomorphologically diverse wetland types.