Hepatitis E virus (HEV) is one of the most common pathogens causing acute hepatitis. Rat HEV, a member of the genus , infects mainly rat but can also cause human zoonotic infection. A survey of the virome of rats via next-generation sequencing (NGS) was performed in Yunnan Province and Inner Mongolia in China. Further screening of rat HEV was conducted by nested PCR. The complete genome of six representative strains were obtained by NGS and RT-PCR. The virome analysis revealed that multiple reads were annotated as . The screening results showed that HEV was detected in 9.6% (34 of 355) of the rat samples and phylogenetically classified into three lineages. The sequences from Yunnan clustered with , named the YnRHEV group, and those from Inner Mongolia were separated into two lineages, named the NmRHEV-1 and NmRHEV-2 groups. Complete sequence analysis showed that YnRHEV had very high sequence identity to a human HEV strain identified in immunosuppressed patients (88.7% to 94.3%) a reminder of the risk of cross-species transmission of rodent HEV. Notably, NmRHEV-1 and the most closely related rat HEV, RtCb-HEV/HeB2014, were divergent from other HEV. The phylogenetic analyses and lower sequence identities of the complete genome suggested the NmRHEV-1 to be a novel putative genus of the subfamily Orthohepevirinae. NmRHEV-2 shared the highest sequence identities (70.6% to 72.0%) with the species , which may represent a putative novel genotype. This study revealed high genetic diversity of in rats in China and a potentially zoonotic strain.