The formation of the modern east-flowing Yangtze River is marked by the incision of the Three Gorges (TG) between the Sichuan and Jianghan basins. However, it is still controversial on the timing of the TG incision, due to diverse tectonic, sedimentological and geochemical records. These records, together with other geological data, i.e. curves of paleo-climate and sea level fluctuation, are critical parameters in the software Badlands , a tool to simulate large-scale and long-term geomorphic evolution. Using Badlands , we modeled the geomorphology and drainage evolutionary process of the Yangtze River since the Late Cretaceous (80 Ma). It revealed that the drainage system in the Sichuan Basin was gradually reversed from southward flowing to northward flowing during the Late Eocene and the Oligocene, due to the periodic uplift of the eastern Tibet Plateau and the southwestern Yangtze Block. Coevally, the Jianghan Basin experienced a base level drop, controlled by the collapse of a paleo-coastal mountain range and the subsequent continental rifting along the Southeast China continental margin. The tectono-geomorphic interplay eventually led to the incision of the TG at the Late Oligocene (about 24Ma), when the drainage system of the Upper Yangtze River was captured by the Middle-Lower Yangtze River.