Objective To analyze the population characteristics of host animals of hemorrhagic fever with renal syndrome (HFRS) from 2009 to 2016 in Anyi county, Nanchang, Jiangxi province, China, and to provide a scientific basis for the prevention and control of HFRS. Methods Snap traps were used for rodent surveillance during March to April and September to October. Direct immunofluorescence technique was used to detect the antigen of Hantavirus in the rodent lung. Related indicators were analyzed with rank correlation. Results Outside the residential area, the rodent population density was 9.93%; Apodemus agrarius was the dominant species with a virus infection rate of 6.16%. In the residential area, the rodent population density was 7.22%; Rattus tanezumi was the dominant species with a low infection rate of 0.32%; Rattus norvegicus was a common species with a relatively high infection rate of 2.88%. HFRS incidence was positively correlated with the rodent infection rate and infection index. Conclusion Apodemus agrarius and R. norvegicus are main hosts animals of HFRS in Anyi county. Rodent control should be strengthened to reduce the risk of HFRS outbreak and epidemics.