This study compared the fungal flora of newly harvested rice in 2017 and that stored for 1 year by traditional culture method and metagenomics techniques. Results showed that the fungi flora in rice changed from various field fungi flora to the storage fungi dominant florasuch as Aspergillus and Penicillium. The results of the two used methods are highly consistent. Exploring the composition and transformations of fungal flora of newly harvested rice and that stored for 1 year can provide important guidance for the prevention of mildew during long-distance transportation.