The Chinese Tianshan is one of the important international natural laboratories for studying continental geodynamics, but its uplift time, kinematics and mechanism of formation are key unresolved questions. In order to constrain the timing, kinematics and mechanism of uplift of the Chinese Tianshan, we applied sedimentary petrography and apatite fission-track dating to Cretaceous-Tertiary series from the northern Tarim Basin and the Tianshan Mountains. We collected and analyzed 79 sandstone samples and 75 detrital heavy mineral samples from the Kezilenuer-Kuqa profile (northern Tarim Basin) with a well-defined magnetostratigraphy. Our data indicate that detrital mineral maturity abruptly decreased at the disconformity between the Upper and Lower Cretaceous, and decreased again after 15(−12) Ma. The sediments in the northern Tarim Basin changed their provenance at 124 Ma, 26(−24) Ma and 15(−12) Ma, respectively. In addition, we collected and analyzed 36 primary apatite samples from the South, Central and North Tianshan. Our results show that the Chinese Tianshan underwent three phases of differential uplift. The first phase of uplift started at the southern Central Tianshan during the Early Cretaceous and propagated southward. The second phase of uplift started at the northern Central Tianshan during the Late Cretaceous and propagated also southward. The third phase of uplift started at the northern Central Tianshan during the Eocene and propagated both northward and southward. These differential uplifts have caused development of disconformity and drops in mineral maturity of detrital sediments in the northern Tarim Basin. Such a differential and heterogeneous uplift process might have been trigged by collisions of different microcontinents (i.e., Lhasa, Kohistan-Dras and India) at the southern margin of Asia. These collisions reactivated the South Tianshan Fault and then the North Tianshan Suture, and uplifted the Chinese Tianshan step by step.