Tobacco root rot disease resistant cultivar Yunyan87 and susceptible cultivar Honghua Dajinyuan ( ‘Hongda’ for short) were used as materials, a pot experiment was conducted to analyze the community structure, diversity and function of fungi in the rhizosphere soils under continuous cropping ( 4 and 8 years) using Ⅰ llumina MiSeq high-throughput sequencing. The results showed that, the relative abundance, diversity indexes, and numbers of endemic species in rhizosphere soil fungal communities of susceptible cultivars were higher than those of the resistant cultivars. Compared to the resistant varieties, the relative abundance of the dominant rhizosphere Ascomycota was higher in susceptible varieties, and those of potential fungi of Mortierellomycota, Basidiomycota, Chytridiomycota were lower at phylum level, while the relative abundance of Penicillium, Chrysosporium, f_Chytridiaceaes were lower at genus level. MetaCyc functional prediction results showed that, with the increase of continuous cropping years, the relative abundance of fungal Fatty acid extension-saturated metabolic pathway decreased first and then increased in rhizosphere soil fungi of susceptible varieties, while that of resistant varieties increased. Under different continuous cropping years, the relative abundance of Fatty acid oxidation Ⅰ, Glyoxylic acid cycle, Pentose phosphate pathway(non-oxidized branch), Calvin cycle, Glycolysis Ⅲ (from glucose), Heme biosunthesis Ⅰ, Coenzyme A biosynthesis Ⅰ and Gluconeogenesis Ⅰ were significantly higher in rhizesphere soil fungal communities of susceptible varieties than those of resistant varieties. In conclusion, reducing the abundance, diversity, relative abundance of metabolic pathways, and increasing endemic species and the abundance of beneficial bacteria are the microbial mechanisms of tobacco varieties Yunyan87 resistant tobacco root rot under long-term continuous cropping conditions.