The study aimed to investigate how mulching practices can improve soil quality by altering microbial community composition and the interrelations among its members. The experiment was conducted for 7 years (from 2012 to 2018) in an apple (Malus domestica cv. Fuji) orchard located on the Loess Plateau, China. Four treatments were applied: conventional tillage (CT), intercrop ryegrass (Lolium perenne L.) cover (RE), inter-row cornstalk mulch (CS), and black ground fabric mulch (BF). The results indicated that compared to CT treatment, all the three mulching practices significantly increased soil moisture content. The RE and CS treatments improved soil organic matter content by 11.8% and 36.5%, respectively, and CS treatment also increased available nitrogen content in soil by 42.0% compared with CT treatment. The soil environmental heterogeneity under different mulching practices shaped the microbial community structure and the dominant populations. All the mulching practices significantly increased the operational taxonomic unit (OTU) abundance and alpha diversity of fungi, and positively affected bacterial richness. Network analyses showed that the microbial structure was significantly affected by soil water and microbial biomass nitrogen. Interestingly, based on network correlation analysis among microorganisms, the BF treatment reduced competition between bacteria, whereas RE treatment increased their cooperation, however, the CS treatment not only promoted cooperation between fungi, but also increased correlations between fungi and bacteria. Finally, our results indicated that mulching practices not only increased the diversity of microorganisms and abundance of dominant species, but also promoted the interrelations among microorganisms in favor of soil quality.