Chiroptera has been identified as a natural reservoir of emerging infectious diseases for carrying zoonotic viruses. An astonishing amount of genetic diversity of viruses has been isolated from the bats in different populations throughout the world. The diversity resource of chiropteran species in Guizhou province is abundant, consisting 65 species, 19 genera and 7 families of 2 suborders. However, there has been limited research on their zoonotic viruses. In this study, 253 faecal samples and 258 bat tissue samples were collected in Guizhou Province, including 10 species in 2 families, 6 genera (S1). Based on viral metagenomics and sRNA virus detection, this research identified the viruses carried by four species of bats that are widely found in Guizhou Province. By analysing different types of bat viruses, and comparing the species differentiation between bats from Guizhou and those from Yunnan and Guangxi, the study detected four types of viruses in four bat species, including vertebrate viruses, insect viruses, plant viruses and bacterial viruses. Furthermore, there were totally 53 families, 111 genera and more than 170 virus species found, including 9 families, 10 genera and 46 species with public health significance, such as Human herpesvirus 1, Hepatitis E virus, Human papillomavirus type 16 (S2). The comparison of virus species among the three regions revealed that only Adenoviridae and Retroviridae were found in the bats inhabiting in all the three provinces, which might indicate that there could be large differences in types of bat viruses distributed in different regions. Since Chiropterans in Guizhou are found to carry a wide range of virus species which have certain representativeness in public health, it is crucial to carry out further molecular epidemiological investigations.