Recently, Influence of human activities and natural disturbances the habitat of Alxa desert in Inner Mongolia was fragmentized, it was lead to the discontinuous distribution of Mongolian Gerbils (Meriones unguiculatus) between habitat patches which might be exist a local population in each one. The precondition of metapopulation establishing was that local population was patchy distribution in discrete habitats. Population dynamics of Mongolian Gerbils were investigated by mark-and-recapture method from 2002 to 2012. This study was conducted in four different habitat patches by different use patterns including a prohibited-grazing site, a rotational-grazing site, an over-grazing site and a farmland. The population spatial structure of Mongolian gerbil was tested whether it had the function of a classical metapopulation, respectively, analysis the population dynamics of Mongolian gerbil, calculation the risk of extinction of local population, Spearman correlations used for determines the degree of population spatial synchrony, and the population turnover rate was evaluated for the dispersal ability of Mongolian gerbil. The results showed that: first, this region was suitable habitats for Mongolian gerbils and the different habitat patches can be occupied by local population, and it was captured two to seven times in eleven years. Second, all the local population had a risk of extinction, and rate of extinction reached 1.000 0 in prohibited-grazing site and rotational-grazing site was higher, the lowest rate of extinction in farmland which was 0.333 4. In the 2008, the largest local population had 26 individuals per hectare in over-grazing site, however, it also suffered from extinction in the 2010. Third, the habitat patches was not too isolated to prevent recolonization of the local population. The Mongolian Gerbils had strong ability of dispersal which the population turnover rate more than 50.0% at most month and especially it reached 100.0% was much more month. Fourth, there was significant positive correlation between rotational-grazing site and prohibited-grazing site in the population density of Mongolian gerbil (P<0.05), but between the others habitat patches had no significant correlation(P >0.05). The Mongolian gerbils population fulfills exceptionally well the four conditions of regional persistence of a species as a classical metapopulation in Alxa desert which has a potential value in small mammal metapopulation research.