Hepatitis E virus (HEV) harbored by small mammals in Dali City, Yunnan Province was investigated. The samples were detected by nested RT-PCR and whole genomes were sequenced by high-throughput sequencing in the positive HEV samples. Bioinformatics was analyzed by the soft-wares of MEGA-X, BESTv1.10.4 and Geneious. A total of 114 small mammals from 6 genera and 7 species were screened in this study. The positivity rate of HEV in Norway rat (Rattus norvegicus) was 8.00% (2/25), and the whole genome of one HEV strain of No. DL147 was obtained, which was the HEV-C1 genotype, and had the highest homology to HEV in the serum of a patient with hepatitis E in Hong Kong, with a nucleotide level of 95.21%. The earliest divergence between the two strains was about 2003. The study confirmed the presence of HEV-C1 infection in Norway rat in Dali City, Yunnan Province, which is highly homologous to the recently reported human emerging HEV and has a relatively recent phylogenetic relationship, and it is instructive for prevention and control of hepatitis E.