The Qinling Shan is located between the North China Craton and the South China Block. Not only is investigating the exhumation process of the Qinling Shan beneficial for comprehending the tectonic collision history of mainland China but also for enhancing our understanding of the development of the Yellow and Yangtze Rivers. Previous studies have predominantly focused on bedrock analysis in the Qinling Shan. However, modern fluvial detrital samples offer a more extensive range of thermal history information. Therefore, we gathered modern fluvial debris samples from the Hanjiang River, which is the largest river in the South Qinling Shan. Subsequently, we conducted apatite fission-track analysis using the laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) method. A total of 214 valid track ages were obtained, with an age distribution ranging from 9.5 to 334.0 Ma. The Density Plotter software was employed to decompose the data and generate four prominent age peaks: 185, 103, 69, 35, and 12 Ma. The exhumation events of the Early Jurassic (185 Ma) and Cretaceous (103–69 Ma) in the Southern Qinling Shan were strongly influenced by the collision between the South China Block and the North China Craton, as well as the subduction of the West Pacific Plate, respectively. The far-field effect of the collision between the Indian Plate and the southern Asian continent influenced the exhumation of the South Qinling Shan during the Late Eocene (35 Ma) and Middle Miocene (12 Ma), respectively. In conjunction with the reported findings, we comprehensively analyzed the geological implications of the Mesozoic and Cenozoic exhumations of the Qinling Shan. The Qinling Shan emerged as a watershed between the Ordos and Sichuan Basins in the early Mesozoic and Cenozoic, respectively. However, the exhumation and expansion of the Tibetan Plateau has forced the Yangtze River to flow eastward, resulting in its encounter with the South Qinling Shan in the late Cenozoic. The exhumation of the Qinling Shan has resulted in fault depression in the southern Ordos Basin. This geological process has also contributed to the widespread arid climatic conditions in the basin. During the Miocene, the Yellow River experienced limited connectivity due to a combination of structural and climatic factors. As a result, the Qinling Shan served as an obstacle, dividing the connected southern Yangtze River from the northern segment of the Yellow River during the late Cenozoic era.