Abstract:[Background] Soil fungi dominate the straw decomposition in the field, and straw incorporation and manure application provide nutrients for fungi. [Objective] To study the effect of long-term straw incorporation and manure application on the soil fungal diversity in the field with winter wheat-summer maize rotation. [Methods] Basing on the 14-year location experiment of straw incorporation and manure application in the field with wheat-maize rotation in southern Shanxi province, the study employed high-throughput sequencing to explore the soil fungal community structure and diversity in response to straw incorporation and manure application. The treatments included straw stubble cleaning+unfertilized control (CK), straw stubble cleaning+N and P fertilizers (NP), straw incorporation+N and P fertilizers (SNP), straw stubble cleaning+N and P fertilizers+manure (NPM), and straw incorporation+N and P fertilizers+manure (SNPM). [Results] The richness, Chao1 index, and ACE index of soil fungi in the treatments with straw incorporation and manure were higher than those of CK. A total of 953 OTUs was detected in the five treatment soils. Specifically, CK, NP, NPM, SNP, and SNPM had 398, 451, 472, 462, and 440 OTUs, respectively. A total of 9 fungal phyla were detected, among which Ascomycota, Mucoromycota, and Basidiomycota were dominant and their abundance were significantly different among treatments. A total of 262 fungal genera were detected, among which the three genera with high abundance were Podospora (18.85%), Mortierella (16.67%), and Fusarium (7.77%) in the CK. The top three common genera with high abundance in NP, NPM, SNP, and SNPM were Dendrostilbella, Botryotrichum, and Mortierella, which showed different relative abundance among treatments. According to the cluster analysis, NPM and SNPM with high similarity in fungal community composition and were classified into one category, while CK, NP and SNP were independent categories. The redundancy analysis with environmental factors showed that total nitrogen content was the key factor affecting soil fungal community structure, which was also affected by available phosphorus, pH, available potassium, available nitrogen, and total phosphorus. [Conclusion] Straw incorporation and manure could alter the soil fungal community structure and diversity in the field with winter wheat-summer maize rotation.