Abstract: In order to explore the new bio-control resources of root-knot nematodes and develop the new bio-control strategies for nematodes, based on the fungal ITS amplicon sequencing technology, the differences of fungal community characteristics between the root system (healthy root HR, non-root knot part of diseased root INR, root knot part of diseased root IRK) and the rhizosphere soil (healthy soil HRS, diseased root soil IRS) of tomato healthy plants and the plants infected by root-knot nematode were compared. The results showed that the healthy root (HR) of tomato was dominated by Glomeromycota, while at the order level, Glomerale was dominant. The diseased roots (INR, IRK) were dominated by Ascomycota. At the order level, the abundance of Glomerales fungi decreased, while the abundance of Hypocreales, Saccharomycetales, Eurotiales and Pleosporales fungi increased. The dominant phylum in the healthy rhizosphere soil (HRS) was Rozellomycota, and the dominant phylum in the diseased rhizosphere soil (IRS) was Ascomycota, among which Hypocreales was the dominant bacteria. The α diversity of fungal community showed that after the root-knot nematode infection, the richness (Chao1 index) of fungal communities in the diseased roots (INR/IRK) decreased, while the richness (Chao1 index) and diversity (Shannon index) of fungal communities in the rhizosphere soil (IRS) were higher than those in the healthy soil (HRS). The β diversity of fungal community showed that the fungal community structure of the five samples was significantly separated. The study showed that the infection of root-knot nematodes will transform the fungi of tomato roots from a symbiotic type dominated by Glomeromycota to an interactive type dominated by Ascomycota, which may be related to the synergistic pathogenicity of specific fungal groups or the recruitment of root-knot nematode antagonistic groups by plants.