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Great gerbil (Rhombomys opimus) colonies, with bare soil and herbaceous plants, are conspicuous to the background environment throughout their range area. In order to quantify the engineer role of great gerbils, we investigated the plant communities of 20 active colonies in the Junggar Basin, Xinjiang, China. In areas without disturbance, desert plant communities were dominated by the shrubs with low level species richness. In burrow areas and surrounding intermediate areas, which were disturbed by great gerbils, the shrubs were suppressed with the decrease of vegetation cover and aboveground biomass. As a result, "niche gaps" were created in disturbed areas and worked as a refuge for herbaceous annuals and perennials. So the existence of great gerbils increased the overall species richness of the desert. Furthermore, herbaceous annuals and perennials are the major food source for great gerbils in spring, indicating that great gerbils have a mutually beneficial relationship with herbaceous plants.