Objective To investigate the pathogen carrier in Inner Mongolia Manchuria port in 2014-2015, in order to provide material basic for further work in epidemic monitoring. Methods To investigate the distribution of rodents, and detect pathogens using PCR or RT-PCR method from May 2014 to April 2015 in Inner Mongolia port areas. Results A total of 828 rodents of 19 species, of which Allactaga sibirica, Spermophilus dauricus, and Cricetulus barabensis accounted for 27.05%(224/828), 23.19%(192/828), and 17.39%(144/828), respectively. There were significant differences in the distribution of rodent species. Detection of Yersinia pestis DNA from the Euchoreutes naso, of Borrelia burgdorferi from Cricetulus barabensis, Euchoreutes naso, Allactaga sibirica, S. dauricus, of Hantavirus from C. barabensis, E. naso, Mus musculus, A. sibirica, and S. dauricus. Conclusion There was a broad and diverse distribution of rodents in the Inner Mongolia. There were also natural infection with Y. pestis, B. burgdorferi, and Hantavirus. In the future, we should strengthen the monitoring and prevention and control of these diseases.