Based on the analysis of heavy mineral assemblages in Cenozoic southwestern Qaidam Basin, we found that different areas have variable heavy mineral assemblage characteristics, which suggested that there were two source areas—the Altyn Mountains and the Qimen Tagh-East Kunlun Mountains. In Ganchaigou-Shizigou-Huatugou(Area A), which was mainly source from the Altyn Mountains, its heavy minerals were mainly composed of zircon, Ti-oxides, and wollastonite in the Paleoceneearly Eocene and mainly of unstable minerals, especially amphibole, in the middle Eocene-Oligene. Since the late OligoceneMiocene, the heavy minerals were still mainly unstable minerals, but the content of epidote increased and the content of amphibole decreased. In Qigequan-Hongliuquan(Area B), which was the mixed source from the Altyn Mountains and the Qimen Tagh-East Kunlun Mountains, its heavy minerals were mainly garnet, epidote, and amphibole. The source of LücaotanDongchaishan-Kunbei(Area C) was mainly from the Qimen Tagh-East Kunlun Mountains, heavy minerals in the sediments in Area C were mainly zircon and Ti-oxides in Paleogene and garnet, epidote, and amphibole in Neogene. In Yuejin-Youshashan(Area D), where the stable minerals and unstable minerals were present simultaneously, the heavy mineral assemblages was controlled by multi-direction source. The variation of heavy mineral assemblages in southwestern Qaidam Basin shows that Altyn Mountains was of low-lying topographic relief in Paleocene-early Eocene, and the rapid uplift of Altyn Mountains started from the middle Eocene. In Paleogene, the Altyn Tagh Fault had a slow strike-slip velocity, but the strike-slip velocity increased greatly since the late Oligocene, leading to a strike-slip displacement above 300 km since Neogene. Meanwhile, the Qimen Tagh-East Kunlun fault zone was under a stable tectonic stage in Paleogene with the Qimen Tagh Mountain being lowlying hills; since the late Oligocene, the fault zone started to activate and the Qimen Tagh Mountain began to uplift rapidly. Based on the analysis of heavy mineral assemblages in Cenozoic southwestern Qaidam Basin, we found that different areas have variable mineral assemblage characteristics, which suggested that there were two source areas-the Altyn Mountains and the Qimen Tagh-East Kunlun Mountains. In Ganchaigou- Shizigou-Huatugou (Area A), which was mainly source from the Altyn Mountains, its heavy minerals were mainly composed of zirconium, Ti-oxides, and wollastonite in the Paleoceneearly Eocene and mainly of unstable minerals, especially amphibole, in the middle Eocene- Oligene. Since the late Oligocene Miocene, the heavy minerals were still mainly unstable minerals, but the content of epidote increased and content of amphibole decreased. In Qigequan-Hongliuquan (Area B), which was the mixed source from the Altyn Mountains and the Qimen Tagh-East Kunlun Mountains, its heavy minerals were mainly from garnet, epidote, and amphibole. The source of Lücaotan Dongchaishan-Kunbei (Area C) was mainly from the the Qimen Tagh-East Kunlun Mountains, heavy minerals in the sediments in Area C were mainly zircon and Ti-oxides in Paleogene and garnet, epidote, and amphibole in Neogene. In Yuejin-Youshashan (Area D), where the stable minerals and unstable minerals were present simultaneously, the heavy mineral assemblages was controlled by multi-direction source. The variation of heavy mineral assemblages in southwestern Qaidam Basin shows that Altyn Mountains was low-lying topographic relief in Paleocene-early Eocene, and the rapid uplift of Altyn Mountains started from the middle Eocene. In Paleogene, the Altyn Tagh Fault had a slow strike-slip velocity, but the strike-slip velocity increased greatly from the late Oligocene, leading to a strike-slip displacement above 300 km since Neogene. Meanwhile, the Qimen Tagh-East Kunlun fault zone was under a stable tectonic stage in Paleogene with the Qimen Tagh Mountain being lowlying hills; since the late Oligocene, the fault zone started to activate and the Qimen Tagh Mountain began to uplift rapidly.