Abstract: Straw returning is an important farmland management measure to improve soil fertility. Soil saprophytic fungi are the drivers of straw decomposition and nutrient transformation. Understanding the effects of straw returning on soil nutrients and saprophytic fungi in different rotation systems is of great significance to improve the efficiency of straw returning and soil fertility. We examined the changes in soil organic matter, total nitrogen, ammonium nitrogen, nitrate nitrogen, available phosphorus, available potassium, and soil fungal and saprotrophic fungal communities of straw removal (S0) and full straw returning (S1) treatments under wheat-soybean (WS) and wheat-maize (WM) rotations in a 3-year field experiment in the fluvo-aquic soil of Henan Province. The results indicated that straw returning significantly increased the comprehensive fertility index of soil. Straw returning significantly increased the content of soil organic matter, total nitrogen, and dissolved organic carbon; and the improvement effects of straw returning on these three nutrients were better in the wheat-soybean rotation than in the wheat-maize rotation The soil fungal communities were dominated by Ascomycota, Mucormycota, and Basidiomycota. The relative abundance of saprophytic fungi (34.9%–51.7%) was significantly higher than that of pathogenic, symbiotic, and unspecified functional fungi (19.6%–22.3%, 13.3%–19.2%, and 15.3%–24.6%, respectively). In the wheat-soybean rotation system, straw returning increased the relative abundance but decreased the α-diversity of saprotrophic fungi. The enrichment of Coprinellus and Talaromyces had significantly positive correlations with soil comprehensive fertility index, soil organic matter and total nitrogen content. However, in the wheat-maize rotation system, the relative abundance of saprophytic fungi was not significantly increased, while its α-diversity was significantly increased. The relative abundances of enriched saprophytic fungi such as Penicillium, Coniochaeta, Sarocladium, Mortierella, Trichoderma, and Fusarium were not only significantly positively correlated with the soil comprehensive fertility index, soil organic matter, total nitrogen, and dissolved organic carbon contents, but also significantly increased the contents of soil available potassium and available phosphorus (by 20.0% and 54.8%, respectively, compared with straw removal). However, short-term straw returning did not affect the content of soil available nitrogen (ammonium nitrogen and nitrate nitrogen). In conclusion, straw returning enhances the soil comprehensive fertility by regulating the community structure and diversity of saprophytic fungi and driving nutrient transformation and accumulation. Straw returning is more conducive to promoting the retention of soil carbon and nitrogen and increasing the abundance of saprophytic fungi in the wheat-soybean rotation system, while it significantly improves the availability of soil phosphorus and potassium and the diversity of saprophytic fungi in the wheat-maize rotation system. This indicates that the crop rotation model significantly affects the fertility effect and microbial driving mechanism of straw returning.