To explore the original state of fungal community of rice with different water content before warehouse storage, Illumina MiSeq high-throughput sequencing was used to analyze the fungal community structure and diversity of newly harvested early japonica rice from Northeast China with different water content in this study. The result showed that the fungal communities in the two rice samples belonged to 2 phyla, 26 classes, 51 orders, 85 families, 112 genera and 188 species according to the 97% sequence similarity level. At the phylum level, the dominant fungal communities in rice with different water content were Ascomycota and Basidiomycota. At the genus level, the contents of Cryptococcus 0.07% and Papiliotrema 3.81% were relatively high in high-moisture rice and relatively low in low-moisture rice. It was found that there were a large number of the same species in rice with different water content, but there were differences among species richness. And the species and number of fungi in rice with high water content were higher than those in rice with low water content. Therefore, it could be concluded that the specific bacteria, such as Filobasidium, Sarocladium and Mycosphaerella, which have significant differences between the two groups of rice in water content, can be inhibited by reducing the rice water content. In conclusion, this study provides theoretical support for water control of paddy rice before entering storage.