The importance of forest floor plants (herbs and mosses) and understory communities on soil C dynamics has been grossly understudied in forest ecosystems; however, there is currently very little knowledge on the impact of forest floor vegetation composition on soil organic C (SOC) accumulation and the microbial metabolic processes. To bridge this gap of knowledge, a forest floor vegetation-removal experiment involving nonvascular mosses (Pleurozium schreberi (PS); Rhizomnium tuomikoskii (RT); and Hylocomiastrum pyrenaicum (HP)) and vascular sedges (Carex sp., CS) was conducted in a subalpine coniferous forest on the eastern edge of Tibetan Plateau, to investigate the associations of different forest floor vegetation communities with mineral soil C accumulation and microbial physiology (C use efficiency (CUE) and microbial biomass turnover). Soils beneath the forest floor vegetative communities differed in soil C and nitrogen (N) concentrations and had distinctively different microbial community structure and physiology. Compared to bare soils, sedge soils had significantly greater SOC and dissolved organic C (DOC) accumulation, greater microbial DNA, biomass C and phospholipid fatty acids (PLFAs) concentrations, and higher microbial CUE and shorter microbial biomass turnover time. While effects of mosses differed among species, P. schreberi had similar effects as sedges, but the effects of H. pyrenaicum and R. tuomikoskii were minimal. Relative to bare soil, P. schreberi and Carex sp. soils were 61.5% and 51.6% higher in microbial CUE and had an obviously shorter microbial biomass turnover time. Variations in the level of DOC and PLFAs (rather than their portion relative to SOC) were the most important regulators of microbial CUE and biomass turnover rate in soils with different forest floor vegetation covers. These results highlight how differences in soil organic matter quality that are directly related to the forest floor vegetation community influence the microbial CUE and biomass turnover and the long-term soil C dynamics.