Shrub encroachment in grasslands will lead to a mosaic landscape with shrub patches interspaced with grass patches and thus alters local and regional water and heat balance. Syntheses on effects of the climate and native grassland community on the shrub-encroached grassland (SEG) are very limited at a large scale. In this study we examined the variation of their community characteristics in the Inner Mongolian grasslands, using 192 SEG plots data from field survey  during 2012–2013. Our results indicated that shrub cover and patch size exhibit a significant increase with longitude, but showed a hump-shaped latitudinal pattern. Shrub patch density and herb abundance were negative associated with latitude and longitude, whereas plant height showed an opposite trend. Such geographical patterns were likely co-determined by climate and native vegetation. Precipitation was the major controller for shrub cover and patch size, and temperature was the primary factor influencing shrub height and patch density. Consequently, shrub cover and patch size were greater at dry and warm habitats than at moist and cool sites. In addtion, native vegetation also significantly influenced the variations in that of shrub patches. Diverse habitats with tall vegetation were likely more resistant to shrub encroachment. Furthermore, although we did not fully evaluate the effects of soils on SEGs, the discussion on the soil-SEG relationship suggests an important role of soils in characterizing SEG structures. Our study provides the first regional assessment on the variations of SEG structures, and has an implication in the regional shrub expansion management and control.