The Cenozoic source-to-sink history of the Qaidam Basin is crucial for understanding of the basin-filling architecture, mountain-building processes and even the dynamics of the Tibetan plateau growth. However, the provenance history of Cenozoic strata in the Qaidam Basin remains ambiguous, especially in the northern Qaidam Basin. This controversy highlights the importance of obtaining the spatial source-to-sink relationships between the Qaidam Basin and its surrounding mountain ranges. In this study, we investigated the detrital zircon U–Pb ages of modern fluvial systems draining the Eastern Kunlun Shan. Their detrital zircon age distributions fall into five age groups: 300-190, 530-360, 1000-560, 2000-1100 and 2650-2000 Ma. The dominant age groups are 530-360 and 300-190 Ma, which represent the successive subduction of the Proto-Tethys and Paleo-Tethys Oceans and the subsequent continental collisions, respectively. Combining these new detrital zircon U–Pb ages with available age datasets, we finally obtained complete detrital zircon age information for modern fluvial systems in the whole Qaidam Basin. The U–Pb age distributions of modern river sands reveal that the zircon age signature of basement rocks in the Eastern Kunlun Shan is significantly different from that in the South Qilian Shan but is similar to that in the Altyn Tagh Shan. Moreover, these zircon age observations were confirmed by the significant difference in the Nd isotopic signature of modern river sands, which reveals a significant difference between the Eastern Kunlun Shan and South Qilian Shan in the formation and evolution process.