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 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. The soil fungi communities were dominated by Ascomycota, Mucormycota, and Basidiomycota, with the relative abundance of saprophytic fungi ranging from 34.9 to 51.7%. 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. To sum up, crop rotation and straw returning synergistically affected the abundance and diversity of saprotrophic fungal communities and promoted the increase of soil nutrients.