Soil microbes are crucial for improving soil quality and productivity. Plastic film mulch (FM), in conjunction with fertilization, has significantly improved crop yields over vast areas of dryland production. However, how these practices affect soil microbial communities, especially as regards co-occurrence patterns within microbial taxa, is unclear. The objective of this study was to determine the effects of 10 years of FM and four nitrogen (N) fertilization rates [0 (N0), 100 (N100), 250 (N250), and 400 (N400) kg N ha−1] on soil bacterial and fungal diversity, community structure, composition, and the co-occurrence network in a rainfed maize (Zea mays L.) field on the Loess Plateau of China. Results showed that N fertilization and FM did not affect soil microbial biomass carbon, but these practices changed the soil bacterial and fungal community structures. The bacterial community structure was dominantly affected by N fertilization, owing to the increased soil N content and decreased soil pH, which reduced bacterial community diversity and altered the relative abundance of some copiotrophic/oligotrophic taxa (e.g., Gemmatimonadetes, Acidobacteria, Rokubacteria, and Planctomycetes). Plastic mulch played a greater role in regulating the fungal community structure, primarily because FM increased soil moisture and promoted soil organic matter decomposition, thereby reducing fungal richness and altered the relative abundance of Chytridiomycota, Mortierellomycota, Glomeromycota, and Mucoromycota. Moreover, FM mediated the effects of N fertilization by reducing soil N content, and then increased the N threshold that caused changes in microbial structure. Network analysis indicated that FM caused an unstable co-occurrence network with fewer positive and negative links, while N fertilization increased both positive and negative (except N400) links, indicating enhanced cooperation and competition among microbes. These results indicate that long-term plastic mulch and high N fertilization could result in risk for soil quality in terms of soil microbial community structure and stability, suggesting that developing new management strategies is necessary to sustain dryland productivity.