Variation of soil moisture affect the structure and diversity of fungal communities. Therefore, in-depth research on soil fungal community under drought stress has important theoretical and practical significance for the western foothills of the Great Xing'an Mountains. We controlled the moisture content of the soils retrieved from the western foothills of the Greater Khingan at 20%, 15%, 10%, 5% and 0%, respectively, simulating drought stress scenario. A total of 3091 OTU sequences with 97% similarity were found by clustering, scattered in 8 phyla, 30 classes, 101 orders, 196 families and 308 genera, mainly in the phylum Ascomycetes, Basidiomycetes, Chytridiomycetes and Glomeromycota, with the highest relative abundance of 70.07% in Ascomycetes.W20 had five biomarkers, W15 had one, W10 had eight, W5 had three, and W0 had four. Drought stress reduced the abundance of Ascomycota, Zygomycota, Basidiomycota, and Glomeromycota substantially. Among them, Ascomycota showed a large increasing trend as drought stress increased, which may be attributed to Ascomycota's high species variety and evolutionary pace, which is more adapted for arid environments. The quantity of Fusarium, Chaetomium, monograhella, Trichoderma, Cercophora, Alternaria, Talaromyces, Conocybe, Amanita, and tomentella was considerably impacted by drought stress. Fusarium's relative abundance increased, then decreased, and then increased as drought stress increased, indicating that it has a strong adaptability to drought. It can cause plant root rot and other diseases, but Fusarium can also secrete cellulase, which plays a role in decomposing soil carbon, and participate in the dissolution of soil insoluble phosphorus with Penicillium, so as to improve phosphorus absorption and utilization by plants.