Four site types, under different kinds of disturbed habitats, were selected in the typical region of the Alashan Desert of Inner Mongolia; this selection dates back from April to October 2002, 2003 and 2004 respectively, i.e. a farmland area, a rotational-grazing area, a over-grazing area and a prohibited-grazing area. The rodent communities fluctuating tendency was studied by using mark-recapture and trap-day methods. The four kinds of mark-recapture sites and that of line sites were taken in different disturbance areas. The area of the mark-recapturing site was 0.95 hm2 and the line site 10 km2. The samples were collected every month in the mark-recapturing sites for 4 consecutive days and in line sites in April, July, and October every year. The variable matrix was composed of captured numbers of the rodent communities. The relationship between rodent communities and plant ones was analyzed with Canonical Correlation Analysis (CCA) under different disturbances. The results shows that the relation between the rodent communities variables and herbage ones of plant communities is significant, on two scales in three years, under different disturbances excepting over-grazing area of marking sites, where 7 of the 8 sites analyzed are closer with herbage in two scales. The relation between the rodent community′s variables and the coverage, biomass above ground of herbage ones is negative. This shows that the coverage and biomass above ground of herbage took a key effect to pattern and dynamics of rodent communities under 4 different disturbances in desert ecosystem. The coverage values and biomass above ground of herbage are higher, and those of richness and biomass of rodent communities composition species are lower. Under the same disturbance, on two scales, the main characteristic of mutuality between rodent communities and plants is as follows: In farmland and prohibited areas, the mutuality between hydrophilic species (Cricetulus barabensis and Spermophilus dauricus) and vegetation is significant. In rotational-grazing and over-grazing areas, the mutuality between xerophilic species (Dipus sagitta and Phodopus roborovskii) and vegetation is very indicative. And above mutuality between animal species and herbage of vegetation is negative.