Tillage rotation is extensively used for wheat-fallow cropping in the drylands of northern China, altering soil compaction, and water availability. However, the roles of tillage rotation in the composition and structure of rhizosphere soil fungal communities remain unclear. High-throughput sequencing technology was used to investigate effects of different tillage rotations, including the control with no-tillage-no-tillage (NT-NT), subsoil-deep tillage (SS-DT), subsoil-subsoil (SS-SS), as well as deep tillage-deep tillage (DT-DT), during the wheat-fallow period on fungal diversity and community structure in the rhizosphere soil. The soil fungal diversity and composition structures under SS-SS showed similarities with NT-NT indicating that SS-SS had disturbed the soil fungal community less than other technologies. The fungal structures were similar in DT treatments (SS-DT and DT-DT) and caused higher soil, with Basidiomycota, Zygomycota, as well as Ascomycota as the most abundant phyla. The relative abundance of dominant genera was 73.1% in NT-NT, SS-SS increased the abundance to 86.9%, while SS-DT and DT-DT decreased the abundance of dominant genera. SS-SS significantly reduced the abundance of Pathotroph (Aspergillus and Bipolaris) and Pathotroph-Saprotroph-Symbiotroph fungi (Alternaria, Acremonium, Fusarium, Entoloma, and Pyrenochaetopsis). These findings suggested that tillage rotation can affected soil fungal community by altering available nitrogen (AN), soil organic matter (SOM), nitrate-nitrogen (NO3-N), as well as ammonium-nitrogen (NH4-N). This approach could have significant implications for sustainable dryland agriculture and farming practices.