Abstract: Selenium-melon is an important cash crop in Ningxia, but its yield and quality decrease when continuously cropped. The decrease may be related to soil fungal community changes that take place during continuous cropping, which was determined in this study. Soil samples from continuous cropping of selenium-melon were analyzed using Illumina Miseq high-throughput sequencing. The analysis showed that, after an initial increase, the diversity and density of the fungal community in the soil of continuous cropping decreased. Eight fungal phyla, 25 classes, and 244 genera were identified in the soil samples. Ascomycota and Zygomycota were the predominant phyla, accounting for > 90% of the fungi. The abundance decreased 32.51% for Ascomycota, but increased 29.89% for Zygomycota, after 30 years of continuous cropping. The most predominant genera were Mortierella, Metarhiziun, Pseudallescheria, Fusarium, and Penicillium, and the abundance changes included a 45.81% increase for Pseudallescheria after 5 years, a 26.74% increase for Fusarium after 10 years, a 26.83% decrease for Metarhiziun after 15 years, a 29.68% increase for Penicillium after 20 years, a 18.30% decrease for Metarhiziun after 25 years, and a 29.89% increase for Mortierella after 30 years of continuous cropping. Soil physical and chemical properties were not related to years of continuous cropping, but affected the fungal community structure. Soil total phosphorus, alkaline nitrogen, and available phosphorus were the most influential factors for fungal genus changes. A significant positive correlation was observed between the abundance of Metarhizium and soil total potassium, between the abundance of Pseudomycetes and soil total phosphorus and available potassium, and between the abundance of Penicillium and soil pH, whereas a significant negative correlation was observed between the abundance of Fusarium and soil total phosphorus and alkali-hydrolyzed nitrogen. Diminished production of selenium-melon in continuous cropping was related to soil fungal community changes rather than soil physicochemical properties, demonstrating that selenium-melon soil-borne diseases might be controlled through biological means.