[Background] Rodent-borne diseases are a class of zoonoses harmful to humans. The epidemic areas of rodent-borne diseases keep expanding with the progress in globalization, and a variety of new rodent-borne diseases emerge while the old infectious diseases reoccur. [Objective] To investigate the prevalence of common rodent-borne pathogens in rodents in Altay prefecture of Xinjiang, and to provide a scientific basis for the prevention and control of local natural focus diseases. [Methods] The spleen and kidney tissue samples were collected aseptically from the rodents captured by night trapping method, and the genome DNA was extracted. Six common rodent-borne pathogens including Bartonella spp., Leptospira interrogans, Orientia tsutsugamushi, Rickettsia mooseri, Anaplasma phagocytophilum, and Francisella tularensis were detected by fluorescence quantitative polymerase chain reaction (qPCR) with TaqMan probe. Illumina sequencing and Nanopore sequencing after routine PCR amplification with universal primers for the 16S rRNA gene were employed to further detect the pathogens. Meanwhile, the spleen tissue was used for the isolation and culture of Bartonella in vitro. The results of qPCR, 16S rRNA gene sequencing, and bacterial isolation and culture were compared. [Results] A total of 66 rodents of 8 species were captured, of which 31 (46.97%) rodents were Apodemus uralensis, and the rest were Rattus norvegicus, Mus musculus, etc. The infection rates of common rodent-borne pathogens detected by qPCR were as follows: Bartonella 31.80% (21/66), L. interrogans 1.50% (1/66), O. tsutsugamushi 1.50% (2/66), R. mooseri 3.00% (1/66), and F. tularensis 13.60% (9/66). A. phagocytophilum was not detected. The Illumina sequencing of 16S rRNA gene detected pathogens (mainly Bartonella) in the 23 samples passing the quality control. The Nanopore sequencing of 16S rRNA gene detected Bartonella in 11 samples passing the quality control, and did not detect the other 5 common rodent-borne pathogens. Bartonella was isolated from 11 spleen tissue samples, with the infection rate of 16.67% (11/66). [Conclusion] Rodents in the Altay prefecture of Xinjiang can carry a variety of rodent-borne pathogens such as Bartonella. We should pay attention to and strengthen the prevention and control of related infectious diseases in this region. Quantitative polymerase chain reaction, bacterial isolation and culture, and 16S rRNA gene sequencing can complement with each other to provide a comprehensive understanding of the local rodents carrying pathogens.