For sandstone-type uranium deposits, an unobstructed recharge-runoff-discharge (RRD) groundwater system strongly constrained by tectonic events is one of the most important cornerstones for uranium mineralization. Junggar Basin, located in NW China, is proposed to be an intracontinental Mesozoic basin with great sandstone-type uranium metallogenic potential but no large uranium deposits so far. Compared with other uranium-bearing basins in Northern China, the Junggar Basin experienced episodic strong tectonic events in the Meso-Cenozoic era, resulting in more intense stratigraphic deformation and dislocation, so the detailed analysis of tectonic evolution and ore-controlling structures is indispensable to deciphering the uranium mineralization process in the region. This study interprets the seismic profiles and analyzes the apatite fission track (AFT) thermochronological signatures of the Jurassic Toutunhe Formation detrital sediments in the eastern Junggar Basin, which reveals that the Junggar Basin experienced four tectonic events: the Middle Triassic-Early Jurassic episodic uplift of basin margin (ca. 240–180 Ma), the Late Jurassic or Early Cretaceous modest deformation and uplift within the basin (ca. 140 Ma), the Late Cretaceous-Paleocene rapid uplift (ca. 100–60 Ma), the Eocene-Present episodic rapid uplift (ca. 38–0 Ma). On this basis, the tectonic couples comprising tectonic window and structural pattern is dissected. The ore-controlling structures that can build the good RRD system are identified, such as Jurassic slope in the eastern Luliang Uplift, Jurassic hanging wall of fault propagation fold, Neogene foredeep of the foreland basin, and so on. Meanwhile, the rapid uplifts in ca.100–60 Ma and ca.38–0 Ma are ascertained as the key tectonic events constrained uranium mineralization. Afterward, a uranium metallogenic model based on the thread of basin tectonic evolution is established, which is of great significance for further deployment of uranium exploration in the basin.