Objective To investigate the differences in fungal community structure and mycotoxin contamination during different shelf-life stages of postharvest longan.Methods Illumina MiSeq high-throughput sequencing technology was used to analyze the fungal diversity of postharvest longan under room temperature storage (25 ℃) and cold storage (4 ℃). Meanwhile, ultra-high-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was used to analyze the levels of 44 mycotoxins in longan samples to identify potential toxin-related hazards.Results With the extension of shelf life, the fungal diversity and richness of postharvest longan fruit under room temperature storage showed a trend of first increasing and then decreasing, while under cold storage, it showed a trend of increasing, then decreasing, and increasing again. At the genus level, Lasiodiplodia was the dominant genus during the early (1~2 d) and late (6~7 d) stages of room temperature storage, with relative abundances ranging from 77.55% to 99.46%. Under cold storage, Candida and Torulaspora were dominant during the middle (10~18 d) and late (21~24 d) stages, with relative abundances of 78.22% and 12.62%, respectively. Mycotoxin analysis showed that no mycotoxins were detected during either room temperature or cold storage.Conclusion The pulp of postharvest longan exhibits a low risk of mycotoxin contamination under both room temperature and cold storage conditions. Spoilage during the shelf life of longan fruit is mainly caused by infection with Lasiodiplodia. The extended shelf life under cold storage is primarily due to the inhibited growth of Lasiodiplodia.