Soil microorganisms play an extremely important role in maintaining the structure and function of the forest ecosystem. The management of Cupressus chengiana plantations is an important silvicultural measure to improve the ecological and economic benefits of plantations and promote the health and stability of ecosystems. However, few studies have focused on its effects on soil microbial community structure. In this study, the C. chengiana plantations in the arid valley of Minjiang River were selected as the research object, the changes of soil physical and chemical properties and microbial community structure under different restoration years (5 years and 9 years) and management regimes (pruning, understory removal, pruning + understory removal) were discussed by using phospholipid fatty acid (PLFA) technology, and their main influencing factors were analyzed, in order to provide scientific basis for the management of C. chengiana plantations. The results showed that the soil organic carbon (SOC), total nitrogen (TN), carbon to phosphorus ratio (C/P), and nitrogen to phosphorus ratio (N/P) of the 9-year restored plantation were significantly higher than those of the 5-year restored plantation (P<0.05), and the total potassium (TK) decreased significantly (P<0.05). Compared with the control, pruning had no significant effect on soil physical and chemical properties, but understory removal and pruning + understory removal significantly reduced the soil water content (SWC), SOC, TN, C/P, and N/P (P<0.05). In addition to the evenness index, the microbial diversity index after 9 years of restoration was significantly higher than that after 5 years of restoration (P<0.05), while the management regime had no significant effect on microbial diversity. The total PLFAs, various groups of PLFAs, various groups of bacterial PLFAs, the ratio of fungi to bacteria, and the ratio of cyclopropane to monounsaturated fatty acids of the 9-year restored plantation were significantly higher than those of the 5-year restored plantation (P<0.05). Pruning increased the total PLFAs and various groups of PLFAs (P>0.05), while different management regimes significantly increased the ratio of fungi to bacteria (P<0.05). Principal component analysis showed that the first and second principal components together explained 66.63% of the total variation in microbial community structure. Restoration years and understory removal significantly altered the microbial community structure, while pruning and pruning + understory removal had no significant effect. Based on redundancy analysis, SOC, TK, and C/P were identified as the main driving factors influencing microbial community characteristics. With the extension of the restoration years of C. chengiana plantation, soil fertility, microbial diversity, and biomass have been improved, and the ecosystem is in a stable restoration process. Although the soil fertility after pruning has not been significantly improved, it has improved the microbial biomass to a certain extent, while maintaining a high vegetation productivity, which can provide a scientific reference for the management of C. chengiana plantation.