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 under different rotation systems is of great significance to improve the efficiency of straw return and soil fertility. We examined the changes of soil organic matter, total nitrogen, ammonium nitrogen, nitrate nitrogen, available phosphorus, available potassium, and soil fungal and saprotrophic fungal communities under the treatments of straw removal (S0) and full straw returning (S1) under wheat-soybean (WS) and wheat-maize (WM) rotations in a 4-year field experiment in Henan province. The results indicate that straw returning significantly increases the soil comprehensive fertility index. Straw returning significantly increased the contents of soil organic matter, total nitrogen, and dissolved organic carbon by 5.8%, 7.6%, 10.5% and 4.9%, 5.7%, 7.1% in the wheat-soybean and wheat-maize rotations, respectively. In addition, straw returning significantly increased ammonium (29.1%), available potassium (20.0%) and available phosphorus (54.8%) in wheat-maize rotation. However, short-term straw returning had no significant effect on the contents of ammonium nitrogen and nitrate nitroge. The soil fungi communities were dominated by Ascomycota, Mucormycota, and Basidiomycota. The proportion of saprophytic fungi (with a relative abundance of 34.9~51.7%) was significantly higher than that of pathogenic, symbiotic, and unspecified functional fungi (with relative abundances of 19.6~22.3%, 13.3~ 19.2%, and 15.3~24.6%, respectively). In wheat-soybean rotation, straw returning increased the relative abundance of saprotrophic fungal community but decreased its α-diversity. The enrichment of Coprinellus and Talaromyces were significantly correlated with soil organic matter and total nitrogen. However, in wheat-maize rotation, the relative abundance of saprophytic fungal community was not significantly increased, while its α-diversity was significantly increased. The enriched Penicillium, Coniochaeta, Sarocladium, Mortierella, Trichoderma, Fusarium were positively correlated with soil organic matter, total nitrogen, ammonium nitrogen, available phosphorus, available potassium. In conclusion, straw returning enhances the soil comprehensive fertility by regulating the community structure and diversity of saprophytic fungi, 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 wheat-soybean rotation, while straw returning significantly improves the availability of soil phosphorus and potassium and the diversity of saprophytic fungi in wheat-maize rotation. This indicates that the crop rotation model significantly affects the fertility effect and microbial driving mechanism of straw returning.