Objective: To investigate the infection status of rodent-borne pathogens among small mammals in the human settlements of Linhai, Zhejiang Province, China, so as to provide a scientific basis for the prevention and control of rodent-borne diseases in the city. Methods: From 2022 to 2024, small mammals were monitored by night cage-trapping in the human settlements, including residential areas, shrublands, and key industries where small mammals are frequently active, across four sub-districts (towns) in Linhai. The liver, kidney, spleen, and lung tissues were collected from the captured small mammals. Fluorescent quantitative real-time PCR was used to detect five rodent-borne pathogens, including Hantavirus, Dabie bandavirus, Leptospira, Rickettsia typhi, and Orientia tsutsugamushi. The positive rates of pathogens in small mammals were compared by species and districts using the χ2 test or Fisher's exact test. Results: A total of 317 small mammals were captured, with a total capture rate of 6.43%, and the most was Rattus norvegicus (187/317, 58.99%). Among 317 samples, 34 were pathogen-positive, with a total detection rate of 10.73%. Leptospira and Hantavirus were the main pathogens, with detection rates of 10.41% and 0.95%, respectively. Leptospira was detected in R. norvegicus, Apodemus agrarius, R. losea, R. tanezumi, and Niviventer confucianus, with positive rates of 8.56%, 48.00%, 7.69%, 5.88%, and 6.25%, respectively. The difference in the positive rate of Leptospira across those rodent species was statistically significant (P < 0.001). Two R. norvegicus samples were simultaneously positive for Leptospira and Hantavirus, indicating a co-infection rate of 0.63%. Dabie bandavirus, R. typhi, and O. tsutsugamushi were not detected in any sample. Conclusions: Leptospira and Hantavirus are the main rodent-borne pathogens in the human settlement environment of Linhai. The positive rate of Leptospira differs across different rodent species. It is necessary to enhance prevention and control measures against rodent-borne diseases, especially targeting the control of R. norvegicus and A. agrarius.