Soil microorganisms can make up more than 95% of the total soil biomass, and plays important role in decomposition of carbon sources and organic matter. Forest management practices (e.g., harvesting, burning, and thinning) influence the composition of the soil microbial community by affecting habitat and substrate for soil microorganisms directly and indirectly, and hence affect soil carbon process. Quantifying the responses of the soil microbial community to forest management is vital to accurately evaluate forest carbon balance and to reveal the underlying mechanisms of soil carbon process change. Thus, an aerially seeded Pinus massoniana forest was chosen in the Three Gorges reservoir area to evaluate the effects on soil microbial community owing to different forest management practices (i.e., control; shrub-removal:harvesting all shrubs and removing all harvest residues. Harvest strategy 1:15% harvest intensity and removing main harvest residues without leaves and small branches; Harvest strategy 2:70% harvest intensity and the same harvest residue management as that in harvest 1). All experimental treatments were located in similar habitats and consisted of three 20 m×20 m plots. The treatments were conducted in October 2013, and soil samples were collected in December 2013 (2 months post treatments) and December 2014 (12 months post treatments) to analyze soil microbial community by using phospholipid fatty acid (PLFA) methods, and analyze soil chemical properties. The results showed that the total microbial biomass and biomass of all microbial species (except arbuscular mycorrhizal fungi) in shrub-removal, harvest strategy 1 and harvest strategy 2 were lower than those of the control in December 2014. However, there was no consistent rule observed in December 2013. Principal component analysis indicated that all treatments showed no significant change in soil microbial community structure in December 2013; the 2 principal component factors related to microbial community diversity explained 60.90% and 17.40% of the variation respectively. Shrub-removal, harvest strategy 1 and harvest strategy 2 did significantly affect soil microbial community structure in December 2014, and the 2 principal component factors related to microbial community diversity explained 50.40% and 26.70% of the variation respectively. In 2013, 5 PLFAs (Mel 16:0, 16:1w5c, 16:1w7c, al17:0 and 20:1w9c) played a major role in the first principal component, and 7 PLFAs (Mel16:0, 16:1w5c, 14:0, 16:0, cy17:0, 16:1w7c, i14:0) played a major role in the first principal component in 2014. The fungi (20:1w9c) PLFAs played the most significant role in the first principal component in 2013 and was replaced by gram negative bacteria (16:1w7c) PLFAs in 2014. Soil moisture, ratio of soil temperature and soil moisture, and soil microbial quotient (ratio of soil microbial biomass carbon and soil organic carbon) were significant factors regulating soil microbial community structure at different treatment times (P < 0.05), as revealed by redundancy analysis (RDA).