Microorganisms play an important role in regulating biogeochemical cycling in terrestrial ecosystems. Microbial functional structure and related processes are determined by the microbial community. Soil physiochemistry properties affect microbial community structure. Land uses affect soil properties and microbial communities, whereas most of the researches at home and abroad focus on the effect of different land uses on soil properties, and how effect of soil properties variations on microbial community and functional structure under land uses were unclear. In this study, land uses (i.e., bare-land, farmland, and grassland) were selected from the long-field experiment (established in 1984). The experimental plot is located at the Changwu National Field Scientific Observation and Research Station of Farmland Ecosystem in the highland and gully region of Shaanxi Province, which is a dry-farming and rain-fed agricultural area. Soil microbial community structure (16S rRNA and ITS), soil physiochemistry properties have been determined, such as soil bulk density (BD), soil organic carbon (SOC), soil total nitrogen (TN), soil microbial biomass carbon (SMBC), and soil mineral nitrogen (mineral N). We found that there was a significant difference in the relative abundance of microbial communities and functional structure under different land uses. Alpha diversity of soil bacterial community was the highest in bare-land, and followed by grassland and farmland. The relative abundance of Proteobacteria, Actinobacteria, and Ascomycota in the farmland (29.7%, 17.3%, 9.2%) and grassland (29.9%, 17.6%, 5.5%) were lower than in bare-land (31.1%, 18.3%, 27.0%). The relative abundance of chemoheterotrophy and aerobic chemoheterotrophy in the bare-land were significantly higher than those in the farmland and grassland, where nitrification and aerobic ammonia oxidation were significantly lower than those in the farmland and grassland (P<0.05). Saprotrophic fungi were the highest in bare-land, followed by farmland and grassland. Variation of bacterial community structure was influenced by BD, TN, mineral N, C:N ratio, and soil microbial biomass carbon (SMBC), while variation of fungal community structure was mainly influenced by mineral nitrogen. In addition, the functional community structure of both bacteria and fungi were mainly affected by BD, SOC, TN, C:N ratio, and SMBC. Specifically, Proteobacteria, Actinomycetes, Ascomycetes, and Basidiomycetes were more suitable to live in the farmland soil than in grassland. Chemical heterotrophic, aerobic chemical heterotrophic bacteria, and saprophytic fungi, which participated in soil carbon cycle, were mainly enriched in the farmland. Nitrification and aerobic ammonia oxidizing bacteria involved in the nitrogen cycle were mainly concentrated in the grassland. Therefore, the change of soil physiochemistry properties driven by land uses affected the community structure and function of microorganisms. In conclusion, variations of BD, TN, SOC, C:N ratio, SMBC, and mineral N under land uses change dominated the microbial community and functional structure.