A growing consensus is reached that microbes contributes to regulating the formation and accumulation of soil organic carbon (SOC). Nevertheless, less is known about the role of soil microbes (necromass, biomass) in SOC accumulation in different habitat conditions in alpine ecosystems. To address this knowledge gap, the composition and distribution of amino sugars (ASs) and phospholipid fatty acids (PLFAs) as biomarkers of microbial necromass and biomass were investigated in forest, meadow and wetland soil profile (0–40 cm) of Mount Segrila, Tibet, China, as well the contribution of bacterial and fungal necromass to SOC. The results revealed that microbial necromass carbon contributed 45.15 %, 72.51 % and 78.08 % on average to SOC in 0–40 cm forest, meadow and wetland soils, respectively, and decreased with microbial biomass. Fungal necromass contributed more to SOC in these habitats than bacterial necromass. Microbial necromass increased with microbial biomass and both of them decreased with soil depth in all habitats. The necromass accumulation coefficient was significantly correlated with microbial necromass and biomass, affected by habitat and soil moisture. Structural equation model indicated that soil abiotic factors indirectly mediated the accumulation of SOC through microbial necromass and biomass. This study revealed that different habitats and soil depths control considerably soil physicochemical properties and microbial community, finally influencing SOC accumulation in alpine ecosystems, which emphasized the influence of abiotic factors on microbial necromass and biomass for SOC accumulation in alpine ecosystems.