To investigate the impact of tobacco-buckwheat rotation on the soil fungal communities in tobacco-growing areas at different altitudes in Shimen county，three regions with long-term continuous cropping of flue-cured tobacco in Shimen county were selected，and two treatments，continuous cropping of flue-cured tobacco(YY)and tobacco-buckwheat rotation(YQ)，were set up. High-throughput sequencing technology was used to study the diversity，structure and function of the soil fungal communities of continuous cropping of flue-cured tobacco and tobacco-buckwheat rotation in different areas. The results showed that:the number of ASVs increased in rotation soils compared with the continuous cropping of all three regions.There were significant differences in the composition of soil fungal communities between continuous cropping and rotation.The rotation soil had higher richness and evenness of fungal communities. A total of 14 phyla，50 classes，130 orders，343 families，756 genera，and 1165 species were detected in all soil samples. At the phyla level，Ascomycota was the dominant phyla in both continuous cropping and rotation soil. Rotation reduced the proportion of dominant phylum and increased the number of dominant phylum species，compared with the continuous cropping. Compared with continuous cropping，rotation changed the dominant fungal genera. Rotation reduced the relative abundance of Fusarium，Plectosphaerella，Alternaria，Ceratobasidium，and Bisifusarium，while increasing the relative abundance of Botrytis，Humicola，Cladosporium，Talaromyces and Itersonilia. principal coordinate analysis showed that there were significant differences in the composition of soil fungal communities between continuous cropping and rotation treatments. Line discriminant analysis effect size analysis results showed that the number of differential species in each treatment ranged from 12 to 17. The soil fungi in the continuous cropping and rotation systems of the three regions were functionally classified，and a total of 8 different nutritional types were predicted. The Pathotroph-Saprotroph-Symbiotroph and Saprotroph nutritional types accounted for a relatively high proportion in both continuous cropping and rotation soils，with proportions ranging from 19.74% to 72.09% and from 14.87% to 57.51%，respectively. Rotation reduced the proportion of the Pathotroph nutritional type and increased the proportion of the Saprotroph nutritional type，and introduced the Saprotrophic-Pathotrophic-Symbiotrophic type. In conclusion，the tobacco-buckwheat rotation increased the richness and diversity of soil fungal communities，changed the structure of soil fungal communities，and had a positive effect on improving the soil micro-ecological environment of continuous cropping flue-cured tobacco and alleviating the continuous cropping obstacles of flue-cured tobacco.