The fungal diversity of five sweet fermented oats samples in China was studied by Illumina sequencing. The results showed that the abundance of Mucoromycota and Ascomycota peaked in the oats Tianpei samples, and a bit Basidiomycota were also included. As to genus, Rhizopus had the highest abundance, followed by unclassified_p_Ascomycota, Saccharomyces and Issatchenkia. Principal component analysis (PCA) indicated that five kinds of oats Tianpei samples formed their own fungal clusters. The biomarker taxa of oats Tianpei were identified by Lefse, including Mucor and Pichia. The fungal composition of oats Tianpei was significantlly related to the chemical composition of oats Tianpei (lactic acid, free fatty acid, amino acid, reducing sugar, etc). The fermentation effects of Rhizopus oryzae on the chemical composition of oats Tianpei were studied also. The fermentation of Rhizopus oryzae significantly increased the chemical composition in oats Tianpei. The research provided a theoretical basis for the study of microbial flora, the discovery of related microbial resources, the fermented modification grains, and the improvement of oats Tianpei quality.