Coastal wetlands contain very large carbon (C) stocks—termed as blue C—and their management has emerged as a promising nature-based solution for climate adaptation and mitigation. The interactions among sources, pools, and molecular compositions of soil organic C (SOC) within blue C ecosystems (BCEs) remain elusive. Here, we explore these interactions along an 18,000 km long coastal line of salt marshes, mangroves, and seagrasses in China. We found that mineral-associated organic C (MAOC) is enriched in BCEs dominated by allochthonous inputs and abundant active minerals, leading to an increased proportion of persistent organic molecules. Specifically, soils with large allochthonous inputs (> 50%) are characterized by a substantial contribution of MAOC (> 70%) to total SOC with a notable preservation of lipids (36%) across salt marshes, mangroves, and seagrasses. The burial of allochthonous particles, derived from external sources such as rivers or tidal influxes, facilitates the formation of stable MAOC through binding to mineral surfaces or occlusion within microaggregates. The proportions of particulate organic C (POC) and MAOC are important predictors for molecular compositions of soil organic matter. Lipid proportions within molecular composition decrease as POC and autochthonous C proportions increase. These findings provide new insights into the coupled control over SOC sequestration in BCEs, emphasizing the role of allochthonous inputs, proportions of carbon pools, and persistent organic components.