Although soil microorganisms play a critical role in soil organic matter decomposition, nutrient cycling and ecosystem productivity, we still know very little about how microbial communities are affected by environmental factors and how the structure and function of soil microbial communities influence key soil processes, especially for the arid and semi-arid river valley district. Studies focusing on soil microbial communities under this region are still under-represented when compared to moist forest and grassland ecosystems. Thus, the objectives of this work were to quantify the effects of shrubs on soil physicochemical properties and microbial composition (Phospholipid fatty acid, PLFA), and to find out soil factors that significantly affect soil microbial composition. To achieve this, we investigated the variations of soil properties between dominant shrubs and shrub-interspaces at a set of sites along the mountainous semi-arid valley of the upper Minjiang River, Sichuan Province. The dominant shrubs had significant effects on soil physicochemical properties and microbial composition, while the effects of shrub species seem to be trivial. The soil under shrub canopies had more organic carbon and nutrient resources, higher water content and lower bulk density than those of the shrub-interspaces. The bacterial communities' abundance did not vary significantly between the two types of soil, while fungi and arbuscular mycorrhizal fungi (AMF) tended to dominate under shrubs. Furthermore, the correlation based Principal Component Analysis (PCA) demonstrated a clear dissimilarity of microbial community composition and physicochemical properties between shrub and shrub-interspace soils. Besides, the PCA revealed that the microbial community composition was a more sensitive and effective indicator than soil physiochemical properties in this study. Backward selection procedure and the combined redundancy analysis (RDA) were used to select the most important soil physiochemical variables affecting soil microbial communities. Though the main factors varied among the four sites, the nitrogen (N) associated factors (Total N, Available N and carbon-to-nitrogen ratio) always played a pivotal role in structuring the microbial groups, especially total microbial biomass (total PLFA) and the bacterial groups (Gran-positive (G+), Gran-negative (G-), general bacteria (B), and cyclo bacteria (cyclo)). The correlation between fungi groups (fungi, AMF) and N associated factors was relatively weak. Total phosphorus and carbon-to-phosphorus ratio strongly affected the fungi and AMF groups in Feihong and Mutuo. This may indicate the importance of phosphorus in shaping fungi and AMF communities, as well as the indispensable role that fungi and AMF communities may play in influencing phosphorus availability and cycling. In addition, soil water content exerted effects on the microbial composition in the two relative humid sites, Cuoji and Mutuo. Moreover, pH did not significantly affect microbial communities, though previous studies have pointed out its important role in affecting microbial composition. This may be due to the small variation of pH in this semi-arid river valley. Collectively, the enrichment of soil nutrients and better physical condition under shrub canopies were the main reasons for the difference of microbial community composition between shrubs and shrub-interspaces. Our work demonstrated the important role of shrubs in the semi-arid valley of upper Minjiang River, and provided insights into the nutrient cycling of semi-arid valley. It also revealed the importance of nitrogen and phosphorus for bacterial and fungal communities, respectively. Future studies on the plant-soil relationship in dryland ecosystems should pay more attention to fungi and AMF communities.