Habitat fragmentation has been a hot topic in ecological research field during recent years, and mammals are widely believed as one of the most vulnerable species in the process of habitat fragmentation. In the present study, we studied the population dynamics of Niviventer confucianus in Thousand Island Lake region which consists of a number of islands. From October 2009 to November 2010, we live-trapped two Niviventer confucianus populations in two islands A and B with similar area and environmental situation using capture-mark-recapture (CMR) method, and studied the impact of habitat fragmentation on the population dynamics of Niviventer confucianus. During the study period, the fluctuation of population, turnover rate, time of residency and effects of climate factors on the populations of Niviventer confucianus in both islands were investigated. Our results showed that the population in both islands began to decease when the animal number in the individual population was over 50, suggesting the both islands with similar area and environmental situation have similar environmental carrying capacity. We also found much more Berylmys bowersi and wild boars in island B than those in island A during June to August, indicating higher living pressure for Niviventer confucianus from inter specific competition and predation in island B, which might cause that the population of Niviventer confucianus in island B declined faster than the population in island A after June. Considering the lack of immigration and emigration in the land-bridge islands, which results in that the turnover rates were very low in the two populations, our observation indicates that the interspecific competition and predation may be the main factor affecting the population changes in the islands. In addition, we also observed that the seasonal change in the island environment has a certain impact on the populations of Niviventer confucianus. In the island environment, the population dynamics of Niviventer confucianus has its own characteristics, which verified our assumption that the impact of land-bridge island environment on the seasonal fluctuation of the number of Niviventer confucianus is different from terrestrial environment. Because of the poor living conditions in land-bridge islands, according to our study of the residence time of Niviventer confucianus, we infer that the ecological life of the Niviventer confucianus living in both islands might be only one year, which was significantly shorter than the ecological life of the Niviventer confucianus living in terrestrial environment in previous studies. Considering the shorter life expectancy and smaller body size of the Niviventer confucianus living in islands, they are suggested to have faster generations update to produce more genetic heterogeneity descendants, which could increase the ecological adaptation and promote the evolutionary speed. It was beneficial for the maintenance and growth of Niviventer confucianus populations when the monthly average temperature was 10-22℃, and it was unfavorable when the monthly average temperature exceeded 22℃. The high temperatures and drought might lead to the population decline of Niviventer confucianus in summer.