Microbial communities and their associated enzyme activities play key roles in carbon cycling in ecosystems. Forest thinning is likely to change the soil properties and feedbacks on the structure and function of microbial communities, consequently affecting microbial regulation on the soil carbon process. However, few studies have focused on the mechanism of how thinning affects the quantity and stability of soil carbon. To reveal the influence of thinning on soil carbon and to explore the regulated key factors, this study was conducted in a pure Larix principis-rupprechtii Mayr plantation with different thinning intensity (light, medium, and high) in Shanxi province, China. Soil properties (soil pH, soil water content, soil organic carbon, and soil microbial biomass carbon) were measured. Meanwhile, soil microbial communities were examined with the method of phospholipid fatty acid (PLFA), and soil enzyme activities were measured as indicators of soil microbial functions. The results showed that medium and high thinning has positive effects on soil organic carbon, microbial biomass carbon, soil microbial abundance, and soil enzyme activities. Actinomycetes and gram-negative bacteria were the major factors to affect soil microbial community function relating to carbon decomposition. Soil pH contributed to actinomycetes and gram-negative bacteria through direct influences on arbuscular mycorrhizal fungi. Moreover, there were strong correlations between soil pH and microbial community to control soil carbon turnover. The increasing of soil microbial abundance and the microbial regulation on soil carbon in forest thinning need to be considered for sustainable forest management practices in northern China.