A sandstone-type uranium deposit has recently been discovered at the bottom of the Neogene Shawan Formation, Beisantai area, southeastern Junggar Basin. In this study, optical and scanning electron microscopic (SEM) observations, whole-rock geochemistry, X-ray fluorescence (XRF) mapping of thin sections, and the electron probe microanalysis (EPMA) of uranium minerals were applied, combined with the sedimentological and tectonic background, to investigate the controlling factors of uranium mineralization. Uranium ores are mainly concentrated on the interface between conglomerate and mudstone both macroscopically and microscopically. Among them, the conglomerate with less interstitial matrix, characterized as high primary porosity and permeability, offers essential passageways for the runoff of groundwater. In contrast, the margin of conglomerate adjacent to the barrier, somewhere with sufficient water–rock interactions, good supply of reducing materials, and efficient adsorbents, is favorable for the precipitation and preservation of uranium minerals. Therefore, the combination of perfect permeable layers and barriers improves the mineralization. From the geochemical data, U is positively correlated with redox-active elements such as S, As, Mo, and V, especially for permeable rocks, suggesting a redox-controlled system. This deposit occurs in a weak reducing reservoir, revealed by the primary green color, and the very low Fe2+/Fe3+ values (0.35–0.77). The much higher enriched Mo (5.89–172.5 ppm, mean = 67.04 ppm) than Se (2–17 ppm, mean = 8.20 ppm) in the redox transition zone suggests that the mineralization is processed during the slow and gentle interlayer oxidation. The pyrites replaced by uranium minerals act as significant reductants in U(Ⅵ) reduction, during which S contributes dominantly over Fe revealed from the increased Fe/S values with the decrease in Fe and S contents in coffinite. Results of EPMA chemical dating reveal that the emplacement of uranium ores started at least from 8 Ma, corresponding to the intensive north–south compression event of the basin since 10 Ma. During the second episode of Himalayan movement, the bottom of the Shawan Formation was gradually denudated and outcropped in the north feasible to the formation of interlayer oxidation zone-type uranium deposit in the Beisantai area. The mineralization is a long-term and continuous process that probably persists till the present.