We analyzed the trace and rare earth element contents of the desert sands and loess deposits in the Junggar Basin. Combined with previously published data, and using principal component analysis, our results provide insights into the sand provenances of the Gurbantunggut Desert in eastern Central Asia (CA); the genetic links between deserts and loess deposits in CA; and the specific sources in CA for the aeolian dust in North Pacific Ocean sediments. The results demonstrate the spatial heterogeneity of the geochemistry of sand across the Gurbantunggut Desert. The desert sands in the northern and western parts of this desert are mainly derived from the Altai and Junggar mountains, respectively, as supported by the directions of sand fluxes. However, Beitashan Mountain makes a negligible contribution due to the lack of fluvial transport and westward sand fluxes. However, more sediment samples need to be collected to confirm the contribution of Tianshan Mountains. Our findings also indicate that the Gurbantunggut Desert did not contribute significantly to loess accumulation on the northern slopes of the Tianshan Mountains, in accordance with the weak genetic relationships between loess deposits and deserts in western CA. We attribute this to the limited ability of the CA deserts to produce and supply dust-sized particles. Additionally, using the Metropolis-Hastings sampling approach, we find that the Gurbantunggut Desert is not the source region in CA for the fine dust particles in North Pacific Ocean sediments. Overall, our results contribute to a deeper understanding of the aeolian systems in CA and their impacts on the dust cycle at a hemispheric scale.