Objective To analyze the monitoring results of rodents in Qinling Mountains in Baoji, China and investigate the population distribution and virus carriage of rodents in this area, and to provide a basis for the control of rodents and rodent-borne diseases in Baoji. Methods Night trapping method was used to capture rodents in 6 ecological environments in Qinling Mountains, including broad-leaved mixed forest, valley, peach forest, and fallow land. Results A total of 164 wild rodents (9 species) were captured, with different populations in different ecological environments at different altitudes. In the valley and arable land below 1850 m above sea level, Apodemus agrarius was the dominant species, accounting for 54.23% (77/142) of all captured rodents, followed by A. peninsulae, accounting for 16.20% (23/142). In the mixed coniferous and broad-leaved forest with an altitude above 1850 m, A. chevrieri was the dominant species, accounting for 72.73% (16/22) of all captured rodents, followed by A. peninsulae, accounting for 18.18% (4/22). Of all captured rodents, 17.81% carried viruses; among the positive rodents, hemorrhagic fever with renal syndrome (HFRS) virus was first detected from an individual of A. peninsulae besides A. agrarius. Conclusion There are a variety of rodents as vectors in Qinling Mountains in Baoji, with different populations at different altitudes, which is almost in accordance with the incidence of HFRS.