The community structures of soil nematodes and microbes are closely related to crop health. The differences of soil nematode and microbial community structures in rice-tomato rotation (FS), continuous cropping (FF) and fallow (CK) cropping systems were studied by a field experiment using traditional classification and high-throughput sequencing techniques. The results showed that there were fewer species of plant parasitic nematodes and higher proportion of free-living nematodes in FS. The detection rate of plant parasitic nematodes was the lowest (5) in FS, and the highest (13) in FF, most of which were common genera. The OUTs and community structure of fungi and bacteria were significantly different under different cropping systems, compared with FF, FS and CK increased the abundance of fungi and bacterial species, shared a larger proportion, and had a more similar community composition; α diversity index of microbe was significantly higher in FS than FF. The groups Chaetomium, Talaromyces, Anaerolineaceae and Acidobacteria that are antagonistic to plant parasitic nematodes in FS was higher in relative abundance than FF. FS can greatly reduce plant parasitic nematode, reshape the microbial community, and improve soil quality, thus, it is an ideal measure for the prevention and control of nematode diseases in tomato production.