Grafting is a commonly employed technique for enhancing the yield and improving resistance to biotic and abiotic stress of cultivated plants. However, whether and how continuous cropping of grafted plants affects the composition, function, and stability of the soil fungal community remain poorly understood. In this study, we investigated the effects of planting years (including 0 years (Y0), 2 years (Y2), 10 years (Y10), and 18 years (Y18)) of grafted watermelon on the structure and functional composition of the soil fungal community under field conditions. Compared with the Y0 soil, the Y2, Y10, and Y18 soils exhibited a significant (p < 0.05) decrease in the richness, Shannon index, and evenness (56.8–65.7%, 22.4–46.3%, and 3.8–38.1%, respectively) in the alpha diversity of the fungal community, but a significant (p < 0.05) increase (0.4–1.3 times) in the fungal population. The structure, core and unique microbiomes, and functional composition of the soil fungal community differed significantly across different planting years. The Y2, Y10, and Y18 soils exhibited significant increases (p < 0.05) in relative abundances of Ascomycota and saprophytic fungi and the proportion of core OTUs, but significantly decreased abundances of Basidiomycota, Chytridiomycota, Rozellomycota, pathogenic and symbiotic fungi, and the proportion of unique OTUs when compared with the Y0 soil. The types of potential plant pathogens and their relative abundance were also significantly increased alongside the planting years (among Y2, Y10, and Y18 soils). Furthermore, the results indicated that the continuous cropping of grafted watermelon altered the co-occurrence networks, leading to a reduction in the complexity and stability of the fungal community networks. Overall, our findings suggest that continuous cropping of grafted watermelon may adversely affect the structure and functioning of soil microbial community, eventually decreasing the effectiveness of grafting technology disease control.
