Objective To investigate the community structure, density, and seasonal variation of rodents at national-level surveillance sites in Chongqing, China, and to provide a basis for the prevention and control of rodent-borne diseases. Methods From January to November, 2018, the trap-at-night method and the route index method were used at four national-level surveillance sites in Chongqing. SPSS 25.0 software was used for statistical analysis, and the chi-square test was used for comparison of constituent ratio. Results In 2018, the density of rodents was 0.98% in urban surveillance sites and 0.73% in rural surveillance sites, with a mean density of 1.15% indoors and outdoors, and the highest density was observed in special industries (1.74%). The mean route index of rodents was 1.81/km in the external environment of various places, and the highest index was observed in waste transfer stations and public toilets (2.86/km). The dominant species was Mus musculus in both urban and rural areas, and there was a significant difference in the composition of rodent species between different habitats (χ²=32.814, P<0.001). Conclusion This study provides preliminary results of the rodents in Chongqing, and reasonable prevention and control measures should be adopted based on surveillance results in districts and counties.