Soil fauna are important components in terrestrial ecosystems. Because soil animals are very sensitive to environment changes, they are useful indicators for soil assessing ecosystem health. In alpine meadow ecosystems, soil animals, especially invertebrates and soil dwelling microfauna are disturbed by herbivorous mammals because of their grazing, trampling, and nutrient transfer through feces and urine etc. Here, we report a study showing the effect of plateau zokor disturbance on soil fauna composition and distribution in alpine meadow in Tianzhu County in the eastern Qilian Mountain in China. We used the zokor mound density to represent its disturbance intensity. We selected four paddocks with different zokor's mounds densities to investigate the soil fauna species and habitat characteristics, including soil physical and chemical properties and plant species diversity and biomass. Multiple Regression analysis was used to determine the relationship between the soil fauna diversity and habitat characteristics. Redundancy analysis was used to assess the influence of environmental factors on soil fauna species distribution and composition. The results show that the Valloniidae, Curculionidae and Brachycera larva were the dominant soil fauna group in the study area. The abundance and richness and Shannon index of the soil animal community in the paddock with extreme disturbance intensity were significantly higher than that in the severe disturbance intensity (P<0.05). The soil fauna abundance, richness and Shannon diversity index had a significant negative correlation with soil temperature. Species richness had significantly negative correlation with soil moisture, the species abundance had significantly negative correlation with soil compaction. The Shannon diversity index for plants had significantly negative correlation with richness and Shannon diversity index of soil fauna. Furthermore, the spatial distribution of soil fauna community was significantly affected by soil temperature, compaction and soil moisture at all sites.