To investigate the influence of seasonal dynamics on the endophytic fungal community of Camphora bodinieri with citral chemotype, we employed standardized sampling and high-throughput sequencing to analyze the diversity, composition, and structure of endophytic fungi across different seasons. A total of 1825 Amplicon Sequence Variants (ASVs) were obtained, belonging to 12 phyla, 43 classes, 104 orders, 239 families, 449 genera, and 663 species. Among them, 23 ASVs were shared across all four seasons, suggesting the presence of a core fungal community. The number of season-specific ASVs was highest in autumn (730), followed by summer (336), spring (325), and winter (202). The results showed that season significantly affected the Shannon (F_3,9 = 5.927, p = 0.016) and Simpson (F_3,9 = 4.892, p = 0.026) indices, with the diversity and species richness of endophytic fungi being highest in autumn and lowest in winter. Across different tissues, the similarity of endophytic fungal communities between leaves and stems was comparatively higher than that with roots. Furthermore, different fungal taxa exhibited differential distribution patterns along temperature–moisture gradients. This study explored the seasonal diversity of endophytic fungi in C. bodinieri with citral chemotype, providing a theoretical basis for understanding host–endophyte interactions.