Grass cover may improve soil environmental conditions in apple orchards. However, the mechanisms for how the soil microbial community changes after cover grass treatments are not well understood. In this study, we analyzed soil properties, microbial community diversity and composition in an apple orchard after being covered with native wild grasses for 3 years on the Loess Plateau, China. The ratios of cover grass were 0% (no cover, NC), 20% (low-intensity cover, LIC), 40% (moderate-intensity cover, MIC1), 60% (moderate-intensity cover, MIC2) and 80% (high-intensity cover, HIC). Meanwhile, the relationships between soil nutrients, cover grass properties, and microbial communities was analyzed by redundancy analysis and Pearson correlations. The results showed that cover grass altered the bacterial community composition, and significant changes at the phylum level were mainly caused by Proteobacteria, Bacteroidetes and Chloroflexi. Compared with NC, the abundance of Proteobacteria was lower in LIC, and the abundance of Bacteroidetes was lower in LIC, MIC1 and MIC2, while that of Chloroflexi was higher in LIC. LIC and MIC1 were the only cover grass intensities that altered the soil fungal community composition; there were no significant differences at the phylum level. The changes in the soil microbial community at the given phyla may be related to the change in soil available nitrogen content caused by cover grass. Here, we demonstrate that cover grass changed the soil microbial community, and the changes may be attributed to the given phyla in the bacterial community; soil copiotrophic groups (e.g., Proteobacteria and Bacteroidetes) were found to be at lower abundance in the low-intensity cover grass.