To investigate the impact of continuous cropping on rhizosphere soil fungal community structure and function in different tobacco varieties with varying resistance to root rot, aiming to provide a theoretical foundation for the prevention and management of flue-cured tobacco root rot. To analyze the structure, diversity and metabolic function of rhizosphere soil fungi community of tobacco root rot resistant variety Yunnan87 and susceptible variety Honghu Dajinyuan( hereinafter referred to as ‘Hongda’) under different continuous cropping years by using Ⅰllumina MiSeq high-throughput sequencing technology, and to explore its correlation with soil physical and chemical factors. The results showed that, The relative abundance and diversity of rhizosphere soil fungal community in ‘Hongda’ varieties was found to be significantly higher than those observed in Yunyan87 under different continuous cropping years, with a greater number of endemic species identified compared to Yunyan87; The abundance of Ascomycota in the rhizosphere soil of ‘Hongda’ was higher than that of Yunnan87, and the relative abundance of Penicillium and Chrysosporium was lower than that of Yunyan87 under continuous cropping; The metaCyc functional prediction results showed that the relative abundance of the first 8 kinds of main metabolic pathways of ‘Hongda’ showed an increasing trend with the increase of continuous cropping years, and were significantly higher than that of Yunnan87. The relative abundance of the rhizosphere soil fungal community of Yunnan87 was the highest except for the fatty acid extension-saturation metabolic pathway, which showed an increasing trend with the increase of continuous cropping years. The relative abundance of the other 8 kinds of main metabolic pathways showed a trend of first decreasing and then increasing with the increase of continuous cropping years; Redundancy analysis showed that soil alkali-hydrolyzed nitrogen content an pH were the main driving factors affecting the changes in fungal community structure. In this study, the rhizosphere soil fungal community of the tobacco root rot susceptible variety ‘Hongda’ exhibited high relative abundance, diversity, and metabolic pathway activity under continuous cropping conditions, however, the low presence of specific biocontrol bacteria and beneficial bacteria may contribute to the challenges associated with continuous cropping and weak disease resistance in flue-cured tobacco varieties.