In recent years, zoonotic diseases have triggered several large-scale outbreaks of infectious diseases, highlighting the critical importance of prevention, detection, and diagnosis of zoonotic infections. The agricultural areas of Qinghai are primarily concentrated in the eastern part of the province, where the habitat of Marmota himalayana partially overlaps with human activity areas. This study employed metagenomic sequencing technology to analyze and compare the composition and diversity of intestinal viruses, and their hosts in Marmota himalayana from six regions in eastern Qinghai’s agricultural areas. The results of the study revealed that the predominant viral families were Caudovirales, Fictiviricetes, and Monodnaviria, with viruses at the order level mainly classified into Microvirales and Circovirales. At the family level, the major viral families were Microviridae and Viphaviridae. Most of the annotated viral genes were associated with protein families involved in genetic information processing, signaling, cellular processes, as well as replication and repair functions. Host prediction predominantly identified Escherichia coli from the Enterobacteriaceae family and Brevibacillus laterosporus from the Bacillaceae family as the main hosts. This study reveals the diversity and regional differences of the virome in Marmota himalayana from the eastern agricultural region of Qinghai, suggesting that certain viral families may exhibit geographic limitations and host specificity, providing a crucial foundation for future viral surveillance and pathogenicity research.