Abstract Background Zoonotic viruses originating from small mammals pose significant challenges to public health on a global scale. Insectivores, serving as natural reservoirs for a diverse array of zoonotic viruses, are known to carry a multitude of viral species. However, compared to the extensive research conducted on rodents (Rodentia) and bats (Chiroptera), the role of insectivores in harboring and transmitting unknown pathogens remains underexplored, which may lead to a severe underestimation of their contributions and impact to global public health. Results This study employed a meta-transcriptomic approach to profile the viromes of 214 individual insectivores, encompassing 13 species from the families Soricidae, Erinaceidae, and Talpidae, collected across 12 counties in Yunnan Province, a recognized zoonotic hotspot. Based on virus reads, the analysis identified 42 viral families associated with vertebrates, highlighting significant virome diversity and host-specific viral tropisms among shrews, hedgehogs, and moles, along with notable geographic and environmental specificity of the viruses. Shrews exhibited greater viral richness and abundance compared to hedgehogs and moles, with variations influenced predominantly by host taxonomy, altitude, and geographic location. A total of 114 RNA-dependent RNA polymerase sequences were obtained, leading to the identification of 68 viruses, including 57 novel species. Instances of host jumping were observed in 11 viruses, with potential pathogenic viruses related to Mojiang paramyxovirus and members of the Hantaviridae family. Cross-species transmission was predominantly observed in viruses carried by shrews, while moles may play a pivotal role in facilitating viral transmission among insectivores. Conclusions This study enhances the understanding of the high diversity of mammalian viruses among insectivores in a relatively confined region and underscores the associations between virome composition and related zoonotic risks, providing a foundation for proactive measures to prevent and control the spillover of emerging zoonotic pathogens and potential future outbreaks. Video Abstract