Structure of rodent community reflects the characteristics of ecological environment. This study systematically analyses species distribution patterns and community diversity of the rodents in the Mt. Helan National Nature Reserve, Inner Mongolia, an "isolated island" in Alashan desert area. The reserve is divided into five habitat types, with a total of 18,748 effective clip days in spring, summer and autumn in 2013. Our project captured two hundred-thirty-five rodents, belonging to 13 species, 11 genera, 5 families in 2 orders, in the area, among them Spermophilus alashanicus is the dominant species. The results indicate that the taxa favored for moisture environment and habitat are the main composition of the community, accounting for 54% of the rodents captured, echoing the unique geographical location and environment of the Mt. Helan, where proportion of moisture environment and habitat increases following increased altitude in the middle and low elevations. According to indices of "edge effect", rodents in the deserts of mountain and grassland, and mountain grassland shrub exhibit a higher density of the community than those in other habitats. In addition to environmental factors, such diversity pattern may have been shaped by the two factors: the increasing number of species, and the evenness of species distribution. The results of redundancy analysis show that vegetation height and coverage, shrub (tree) height and altitude, are the most important environmental factors driving the formation of rodent community. Interestingly, different from the others, vegetation coverage is negatively correlated with community diversity index decreases following the increased vegetation coverage.