This study investigated the impact of continuous flue-cured tobacco cropping on soil fungal communities. Using qPCR and high-throughput sequencing, researchers compared fungal abundance, diversity, and composition in soils after 3 years (3ys), 5 years (5ys) of continuous cropping, and a control (CK) with 1 year of cropping. Continuous cropping altered fungal abundance and diversity, increasing the relative abundance of *Mortierellales* (which solubilize mineral phosphorus) but also potentially increasing pathogenic fungi. Available potassium and phosphorus were identified as key soil factors influencing fungal community structure. Long-term continuous cropping resulted in more complex and stable fungal networks.