Abstract: Continuous cropping obstacles occur in foxtail millet. To understand the effects of continuous cropping of foxtail millet on the soil fungal community structure, we explored the distribution characteristics of the fungal community of the rhizosphere soil using the fungal ITS high-throughput sequencing technology under different cropping strategies, including foxtail millet-maize rotation, foxtail millet continuous cropping for three years and five years, and the abandoned land taken as a control. The results showed that a total of ten phyla, 24 classes, 46 orders, 79 families, 136 genera, and 146 species of fungi were detected in the rhizosphere soil of foxtail millet under different cropping strategies. The population structure was relatively stable at the phylum and class levels. The dominant phyla in the soil mainly consisted of Ascomycota and Basidiomycota, whereas the dominant classes were Sordariomycetes, Dothideomycetes, and Pezizomycetes. At the order level, the relative abundance of Sordariales in the rhizosphere of foxtail millet was two times greater than that in abandoned land. At the family and genus levels, the relative abundance of Mortierellaceae and Mycosphaerellaceae was higher, whereas the relative abundance of Alternaria, Didymella, and Clonostachys was lower in the rotation soil than in the continuous cropping soil. Alpha diversity analysis showed that the fungal abundance of the rhizosphere soil was significantly different under foxtail millet-maize rotation and foxtail millet continuous cropping (P<0.05), and that under that rotation, soil diversity was the highest. Beta diversity analysis revealed that the fungal structures of the rhizosphere soil under continuous cropping for three and five years were similar, and they were different from those under abandoned land or rotating cropping, indicating that the fungal community structure in the rhizosphere soil of foxtail millet changed under different cropping strategies. Correlation analysis showed that alkali-hydrolyzed nitrogen was significantly positively correlated with organic matter (P<0.01) and significantly correlated with available phosphorus and urease activities (P<0.05), while the activity of polyphenol oxidase was positively correlated with available potassium (P<0.05) and significantly positively correlated with the Chao1 index and the observed species index (P<0.01). Redundancy analysis (RDA) indicated that CK were affected by Chaetomium, CR was affected by Mycosphaerella and Microdochium, TC and FC were affected by Botryotrichum, Chaetomidium, and Didymella. LEfSe analysis identified distinctly specific markers in the rhizosphere soil of foxtail millet under different cropping strategies. The markers of rhizosphere soil contained Mortierella and Mycosphaerella for the rotating cropping, Botryotrichum, Didymella, and Clonostachys for three years of continuous cropping, and Alternaria and Didymella for five years of continuous cropping. Overall, the soil fungal community structure under millet-maize rotation cropping, exhibiting more saprophytic fungi and fewer pathogenic fungi, was significantly different from that under foxtail millet continuous cropping, which provided useful information for the study of the continuous cropping obstacles of foxtail millet.