Soil organic carbon (SOC) plays a crucial role in mangrove blue carbon formation, yet the differences in microbe-mediated underlying SOC sequestration between introduced and native mangroves remain unclear. Here, we compared the SOC pool, including recalcitrant organic carbon (ROC) and labile carbon pools, as well as three residual carbon sources (amino sugars, lignin phenols, and lipids) in sediments between mangroves of introduced Sonneratia apetala and native Kandelia obovata, and further connected them with microbial life strategies and C metabolism capability. The results showed that SOC accumulation in S. apetala (SA) sediment was about 30%–50% of that in K. obovata (KO) sediment. ROC was the dominant form of SOC in long-term sequestration (76%–83%), while lignin phenols, amino sugars, and lipids were important sources of ROC. In S. apetala sediments, the ROC content was positively correlated with amino sugars, resulting from the more r-strategist microbes that can rapidly convert plant-derived carbon into microbial biomass, which is subsequently transformed into microbial necromass. In contrast, in K. obovata sediments, ROC content showed a stronger positive correlation with the concentrations of lignin phenols and lipids. More K-strategist fungi in the topsoil of K. obovata increased enzyme activities, while more K-strategist bacteria in the subsoil enhanced carbon utilization capacity, thereby increasing lignin phenols and lipids from plant residues in both soil layers. Meanwhile, higher Ca²⁺ concentrations in K. obovata sediments protected three residual carbons from further microbe decomposition. This study provides valuable insights into the molecular mechanisms of SOC sequestration mediated by microbial life strategies in mangrove ecosystems.