Abstract:To investigate the effects of temperature and humidity on bioactive components and fungal diversity in Citri Reticulatae Pericarpium, samples of Citrus reticulata ‘Chachi’ underwent alternating treatments of high temperature and high humidity (35 °C, 85% RH) and low temperature and low humidity (20 °C, 55% RH) for 180 days, with natural room-temperature storage as the control. Samples were collected every 30 days to determine total phenolics, total flavonoids, hesperidin, hesperetin, nobiletin, and tangeretin contents. Antioxidant activity was evaluated using ABTS and DPPH assays. Fungal community succession was analyzed via Illumina MiSeq high-throughput sequencing. Correlation analysis elucidated associations between key fungal genera and bioactive components. Total phenolic and total flavonoid contents declined in both groups. At 180 days, the treatment group showed significantly higher total phenolic content and significantly lower total flavonoid content than the control. The treatment group showed a decrease of 5.90 mg/g in hesperidin, while hesperetin, nobiletin, and tangeretin increased by 0.57 mg/g, 0.60 mg/g, and 0.10 mg/g, respectively, with all changes significantly greater than those in the control (P<0.05). The decline rates of ABTS? and DPPH activities were lower in the treatment group than in the control. Regarding fungal diversity, richness and diversity declined continuously in the treatment group, whereas the control group exhibited alternating increases and decreases. At the genus level, Xeromyces reached a relative abundance of 95.71% at 180 days in the treatment group. Correlation analysis showed that Xeromyces and Clavispora were positively correlated with hesperetin, nobiletin, tangeretin, and antioxidant activity (P<0.05), and negatively correlated with hesperidin. In this study, alternating temperature and humidity treatment was used to simulate the natural aging environment of Citrus reticulata ‘Chachi’. Through 180 days of continuous dynamic monitoring, the relationships among temperature and humidity, flavonoid components, and fungal communities were analyzed, revealing their synergistic changes and providing a reference for optimizing standardized storage processes for Citri Reticulatae Pericarpium.