We live-trapped two Niviventer confucianus populations from October 2009 to November 2010 in Thousand Island Lake region using the capture-mark-recapture (CMR) method, and studied the age structure and sex ratio of the populations. Then, we discussed the impact of habitat fragmentation on the population structure of Niviventer confucianus. Our results showed that the dominant groups included juvenile group and sub-adult group in the first half of the year, while they changed into the adult group and old-adult group after half the year. It was different in the influence on the age structure of Niviventer confucianus between the land-bridge island and terrestrial environment. The juvenile group began to appear in October and November, and the high proportion of juvenile group was in March and April. So the population growth reached the peak in the first half of the year. Because of Aging, the population eventually declined after half the year. There was significantly negative correlation between the population quantity and sex ratio. When the population sizes reached the peak, the number of females was less than that of males. Nevertheless, when the population sizes were low, the number of females was more. We considered that in the process of population growth, the females were more important than males. This may be a performance of the internal adjustment mechanism of population dynamics of Niviventer confucianus. The predation risk is one of the main factors to affect the sex ratio. The wild boar may lead to the fewer males in June in B island. The average litter size of Niviventer confucianus in medium-sized island was significantly higher than that in Jinhua region from September to October. Because of the high breeding rates in September and October, February and March, the population reached to a higher level in the first half of the second year.