Objective To understand the distribution of rodents, dynamics of rodent density and composition in hydro-fluctuation area of Three Gorges Reservoir after experimental storage, and provide evidence for the risk prediction and control of rodent-borne diseases. Methods Four surveillance sites were set in upper, middle and down reaches of the Three Gorges Reservoir and surveillance were carried out twice after water drainage and before water storage every year. The small mammal density and the species composition in different regions, altitude and periods were analyzed. Results During 2010-2014, a total of 116 small mammals were captured and the average capture rate was 1.10% and on the decline overall. The captured small mammals were classified into six species. Apodemus agrarius was the predominant species accounting for 46.55% and Anourosorex squamipes was next with 25.86%. The average capture rate after water drainage (1.23%) was higher than that before water storage (0.90%). All captured small mammals distributed in all three altitude and the composition decreased from high to low latitude. The predominant species was different in three altitude. The predominant species in 166-175 m altitude was A. squamipes accounting for 44.45%, followed by Rattus tanezumi (18.52% ); In 145-155 m and 156-165 m altitude, Ap. agrarius was predominant species accounting for 84.00% and 72.97%, respectively. Conclusion The average capture rate was low and there was various species of rodent in hydro-fluctuation area. The density and species composition of small mammals varies with different regions, altitude and monitoring time. The host animals of hemorrhagic fever of renal syndrome, Leptospinosis and commensal rodent plague may be of risks in hydro-fluctuation area of Three Gorges Reservoir. It should be strengthened to monitor the host animals and take the corresponding control measures in the area based on the risk assessment.