Communities of arbuscular mycorrhizal fungi (AMF) in soil are impacted by agricultural management, which in turn influences crop growth and yield. Yet the combined effects of tillage and fertilization practices upon AMF communities are still poorly understood. This study investigated the interactive effects of tillage (no-tillage and conventional tillage) and fertilization (no-fertilization and biologically based organic fertilization) factors on AMF community structure and yield of winter wheat field. The five-year field experiment was conducted in Longde County, Ningxia, China. Results indicated that no-tillage significantly increased the species richness, evenness, and diversity of soil AMF, whereas bio-organic fertilization was less influential. Under no-tillage, bio-organic fertilization marginally increased the richness and diversity of AMF species; however, under conventional tillage this effect was inversed. Glomus, Claroideoglomus, and Paraglomus AMF genera dominated under no-tillage combined with bio-organic fertilization. No-tillage increased the relative abundance of Glomus, while bio-organic fertilization increased that of Claroideoglomus. Redundancy analysis revealed that total nitrogen and available phosphorus were the most important soil variables related to the diversity and community composition of AMF. The yield of winter wheat was negatively correlated with AMF diversity and positively correlated with Glomus abundance. This study suggests that, compared to single conservation agricultural practices, combining no-tillage with bio-organic fertilization may further improve the benefits of soil AMF for winter wheat crops. However, under low nitrogen and phosphorus inputs, conventional tillage can accelerate the mineralization of organic matter and increase the availability of soil nutrients, thereby improving wheat yield.