Livestock manure contains a high concentration of pathogenic bacteria, viruses, and other harmful microorganisms. The effective elimination of these pathogens is of great significance to the harmless and resource utilization of livestock and poultry manure. Building upon prior research, this study further explored the removal efficiency of pathogenic bacteria and viruses in sheep manure compost on Qinghai-Tibet Plateau under 45 % (M45) and 60 % (M60) moisture content. The results showed that M45 led to a significant increase in the average composting temperature (P<0.05), a notable reduction in the levels of Salmonella and Coliforms in the compost products, and facilitated the decline in abundance of various pathogens. As composting progressed, the abundance of viruses declined rapidly. Uroviricota was the most dominant viral phylum, and Siphoviridae, Myoviridae, Herpesviridae, and Podoviridae as the predominant viral families. M45 can significantly reduce the diversity and abundance of compost virus community (P<0.05). The correlation analysis indicated a negative relationship between pathogens and the average temperature and humus content of the compost. In summary, the reduction of moisture content can enhance the biosafety of sheep manure compost products on the Qinghai-Tibet Plateau. These findings provide theoretical basis and technical support for the harmless and resource utilization of sheep manure waste on the Qinghai-Tibet Plateau.