In order to explore the effects of house warehouse storage on fungal community diversity of imported soybean, Illumina MiSeq high-throughput sequencing was employed to analyze the fungal community structure and diversity of newly harvested imported high oil soybean for 3 months with periodic sampling for moisture determination. The result demonstrated that the fungal communities in different storage periods in the high oil soybean belonged to 4 phyla, 9 classes, 14 orders, 15 families, 21 genera and 19 species in accordance with the 97% sequence similarity level. The four dominant phyla of soybean in different storage periods were Ascomycota, Basidiomycota, Mortierellomyco and Mucoromycota. At the species level, classification statistical analysis showed that the 10 strains with relatively high abundance presented an increasing trend with the extension of storage time (C47>B47>A47). In addition, quarantine pathogenic fungus gibberella were found. Through the analysis of Ven map and Beta diversity, it was found that the fungal community structure of soybean samples in the first two storage periods was relatively similar. The fungal community structure of soybean samples in the third storage period was significantly different from that in the first two storage periods with the storage of house warehouse. It could be concluded that the fungal community diversity of soybean samples in the third storage period not only increased significantly, but also experienced obvious succession of fungal community structure.