Based on the field vegetation investigation of Yihejigede Lake in the Badain Jaran Desert, biodiversity was studied, and the relationship between vegetation and mega-dune morphology was analyzed. The results showed that there were less vegetation types in the study area, mainly composed by xeromorphic species, the vertical distribution and differences of vegetation communities was obvious. Vegetation in the study area belongs to 9 species, 9 genera and 6 families, from the top to the bottom of mega-dunes vegetation communities changed from herbaceous community to shrub communities to herb or subshrub community. Agriophyllum squarrosum distributed in the leeward slope, but Corispermum patelliforme and Artemisia blepharolepis distribuled in windward slope; The overall community diversity showed that diversity index was higher in the middle of both mega-dune slopes, and evenness index was higher in the top of leeward slope and the middle of windward slope. The hierarchical community diversity showed that diversity index and evenness index had little difference for herb community because of the relatively single species, the shrub community in the middle of windward slope had the maximum diversity index. The feature of vegetation communities was affected by the whole morphology of mega-dunes, there existed a well corresponding relation between the vegetation characteristics including distribution and diversity in the windward slope and the physiognomy morphology with order 1 and order 2 of mega-dunes. In a broader development period of desert, the sparse vegetation may play an important role in maintaining the height of mega-dunes through influencing sand transport rate and then intercepting the sand.