A fission track analysis of apatite samples from Cenozoic sandstone near the Kuqa River shows that these samples can be divided into 3 groups, which display the exhumation and cooling of the margin of the Kuqa Basin or the Tianshan Mountains. Based on experimental data and thermal history modeling, it is concluded that the South Tianshan and Kuqa Basin experienced three major uplifting events. The South Tianshan began to uplift at 142 Ma, causing differentiation between the basin and the mountain. The uplifting in 96--75 Ma was a regional event, during which the basin margin and the Tianshan uplifted together. The Tianshan and Kuqa Basin underwent differential uplifting during 54--30 Ma, resulting from ladder-like uplift of basin and mountain.