[Objective] To uncover the risk of rice mildew and ensure cereal security, this study compared the surface and endophytic fungal community characteristics in rice under granary storage and simulated storage with high humidity in Zhejiang to explore the predominant fungi and potential toxigenic fungi under the two storage conditions. [Method] Cultivable molds in rice samples were identified by plate culture, morphological observation, and ITS sequencing, and fungal community diversity of rice was investigated by high-throughput sequencing. [Result] Compared with that at the early storage stage, the mold number of samples during late stage of granary and simulated storage increased by 7.05% and 12.03%, respectively. Although Ascomycota was a dominant phylum in rice under the two storage conditions, the predominant cultivable molds were Curvularia (35.66%) and Penicillium (51.13%), respectively. The relative abundance difference of Penicillium reached 42.7%. Alternaria was a common predominant genus of surface fungi and endophytic fungi in rice under granary storage, and the relative abundance of endophytic Alternaria (39.85%~91.51%) was higher than that of surface ones (14.33%~30.53%). In the rice under simulated storage, Alternaria (<32.32%) was the common predominant genus of surface fungi and endophytic fungi at the early storage stage, while Aspergillus (<15.01%) was the predominant genus after storage for 3 months, which indicated an alteration of predominant fungi during storage. In addition, the relative abundance of Fusarium solani secreting deoxynivalenol (DON) decreased by 3.10% and 2.46% in rice under granary and simulated storage over time, respectively. In addition, Hypocrea, Sarocladium, and Alternaria were identified as marker genera in rice under granary storage, while Wallemia and Aspergillus might be used as marker genera in rice under simulated storage rice at different stages. [Conclusion] The mold number of rice under storage significantly increased, and Alternaria was identified as a predominant genus in rice under both storage conditions. The high humidity increased the relative abundance of Aspergillus in both surface and endophytic fungi. The potential toxin-producing fungi Alternaria and Aspergillus were the two marker genera in rice under the two storage conditions, respectively. The findings provide a theoretical basis for controlling rice mildew and toxin accumulation.