The landscape in desert margin regions is simultaneously shaped by both wind and water forces, resulting in a particular spatial distribution of dunes. It has been suggested previously that aeolian and fluvial systems should be integrated in investigations of the development of regional landforms. We carried out a comprehensive study of landforms on the southern margin of the Taklimakan Desert, China based on remote sensing images, meteorological data and morphodynamic theories of dune formation. Our results indicate that the major characteristic of dunes in this region is the coexistence of dunes with different orientations in a small geographical area. As the development of dunes is mainly determined by the wind regime and the availability of sand, the coexistence of dunes with different orientations might be caused by differences in the availability of sand. The topographic relief and fluvial systems both affect the grain size distribution and the amount of sediment in different regions, resulting in variations in the availability of sand. A comprehensive analysis of the spatial distribution of dunes and the regional environment can help our understanding of the regional variations of sediment in aeolian–fluvial interaction systems and help to model the development of landforms in these environments.