Abstract: Exploring the diversity, composition, and functional characteristics of the phyllosphere fungal community during the air-curing process of cigar leaves is of great significance for revealing the "catastrophic" mechanism of curing and achieving the goal of "mold control and quality enhancement." In this study, ‘Yunxue 2’ (A) and ‘Yunxue 39’ (B) were used as experimental materials. Leaf samples were collected on days 0, 5, 10, 15, and 20 of the air-curing process to analyze the dynamic evolution of the phyllosphere fungal community via high-throughput sequencing. The results indicated that with the progression of air-curing, the contents of total sugar, reducing sugar, and photosynthetic pigments in both cultivars significantly decreased and eventually stabilized. Redundancy analysis (RDA) showed that the relative abundance of Ascomycota was significantly and positively correlated with free amino acid content and the relative humidity of the curing barn. Alpha diversity analysis revealed that the Shannon, Chao1, and PD indices of ‘Yunxue 2’ followed a "decrease-then-increase" trend, whereas those of ‘Yunxue 39’ exhibited an "increase-then-decrease" pattern. Regarding community composition, a distinct divergence in fungal structure was observed between the early (0–5 d) and late (10–20 d) stages of curing. During the early stage (0–5 d), Basidiomycota, unclassified_k_Fungi, and Ascomycota were the dominant phyla; however, Ascomycota became increasingly dominant as the process reached the 10–20 d mark. At the genus level, the abundance of pathogenic fungi such as Alternaria and Fusarium increased and became more evenly distributed. Functional prediction indicated that the trophic types were primarily saprotrophic and pathogenic. In conclusion, the phyllosphere fungal community structure of cigar leaves tends to simplify during air-curing, while the abundance of pathogenic and saprotrophic fungi increases significantly. These findings provide a theoretical basis for elucidating the mechanism of mold spoilage and the micro-ecological regulation of the phyllosphere during cigar air-curing.