Higher aquatic plants and benthic macroinvertebrates of 12 lakes located in Inner Mongolia-Xinjiang Plateau were investigated in July and September, 2008. We have sampled aquatic macrophytes and benthic macroinvertebrates from the elevated 11 lakes, except for Lake Tianchi. A total of 12 species and 8 families of higher aquatic plants, and 64 macroinvertebrate taxa belonging to 26 families, 8 classes and 4 phlums were found. Of which Phragmites australis and Potamogeton pectinatus were dominant plant populations, and Chironomm spp. and Limnodrilus spp. were dominant benthic taxa. Lake Wuiiangsnhai had the highest species richness of 9 of aquatic macrophytes and of 35 of benthic macroinvertebrates. Aquatic macrophytes were distributed in whole lakes in Lake Wuliangsuhai and Lake Hasuhai, but in other lakes they occurred only in some bays. The similarity of benthic macroinvertebrate feunas in 10 lakes was low (Stress value=0.11). Benthos biodiversity in coastal macrophytes area was significantly higher than that in open water area. However, the dominant concentration in coastal macrophytes area was significantly lower than that in open water area. No benthos was found in the strong current water. Community similarity analysis of benthos in different habitats of coastal plant area indicated that the habitat of dense submerged plants area and weak lake current area had the high-est abundance of benthic fauna, while the strong lake current area had no benthic animals. In general, the species similarity of both aquatic plant communities and benthic macroinvertebrate faunas were low in the lakes in Inner Mongolia-Xinjiang Plateau. Our results suggested that the coastal plant area, especially the weak lake current and submerged plant area, is key area to protect in whole lake system.