In hyperarid desert regions, the key factors and mechanisms governing the spatial variations in the composition and ratio of chemical elements in the eolian sediments remain largely uncertain. In this study, a total of 115 samples of eolian sand, lacustrine sediment, and exposed bedrock were collected across the entire Badain Jaran Desert in the hyperarid region of northwestern China and analyzed for major elements and trace elements by X-ray fluorescence spectrometry. The purpose of the study was to determine the main drivers of the spatial variations in the chemical composition of eolian sediments, and to improve our understanding of the complex processes of transport and deposition. Our results show that the elemental concentrations of eolian sediments varied considerably among different regions, particularly between the marginal and central zones, which could be related to differences in the chemical composition of the source rocks. The variations in the chemical composition of eolian sediments in the central zone were affected mainly by sedimentary sorting rather than spatial heterogeneity in precipitation. Given that the changes in Chemical Index of Alteration (CIA) were not a function of the chemical weathering in this desert, the exact environmental significance indicated by CIA should be stated explicitly before using this index as a proxy for paleoenvironmental reconstructions in hyperarid regions.