Global warming is one of the environmental problems that cannot be ignored in the world today, which has significant impacts on soil carbon dynamics and soil microorganisms. Soil microorganisms affect the soil nutrient cycling process and play a leading role in the net carbon balance of terrestrial ecosystems. Further exploration of microbial responses to climate warming is important for predicting the feedback and carbon budget of terrestrial ecosystems in warmer climates. In this study, soil organic carbon content and microorganisms were investigated in a natural warming experiment using a whole ecosystem transplanting approach. Plots of plants and soil in a subtropical mountain evergreen broadleaf forest at high altitude (600 m asl) were moved to low altitude (30 m asl) in Dinghu Mountain to experience natural warming treatment. Plots with similar plants and soil at the high altitude were used as the control. To explore the effect of natural warming on soil organic carbon metabolism and its microbiological mechanism, soil physical and chemical properties, soil organic carbon, and soil microbial community structure were measured for the control and warmed plots. Meta-genomic method was used for soil microbial community structure and abundance of genes involved in soil organic carbon decomposition. Results showed that:(1) warming treatment significantly changed soil temperature and moisture of the 0-10 cm soil layer. From 2016 to 2018, the soil temperature was significantly increased by 2.48℃, and the soil moisture was significantly decreased by 23.93% (relative change). (2) Warming treatment significantly reduced soil organic carbon content in the dry season and the soil nitrate nitrogen content in the wet season, while other soil physical and chemical factors had no significant changes under warming treatment. (3) Warming treatment changed the soil microbial community structure in both dry and wet seasons, and the change was significant in wet season. The results of principal component analysis showed that soil moisture was the main factor affecting the variation of soil microbial community structure in dry season and wet season, which explained the variation degree of 50.2% in dry season and 79.2% in wet season. (4) The metagenomic analysis showed that increasing temperature inhibited the abundance of soil organic carbon metabolism genes of mountain evergreen broadleaf forest in the dry season, and enhanced them in the wet season. Our results showed that although warming treatment did not significantly change soil microbial biomass in the subtropical mountain evergreen broadleaf forest, it reduced soil organic carbon by changing soil microbial community structure and abundance, and significantly affected soil organic carbon metabolic processes and ecosystem carbon cycling.