The Beisantai deposit is a newly discovered typical interlayer oxidation zone-type uranium deposit mainly hosted in distributary channel conglomerates of the Neogene Shawan Formation in East Junggar Basin, northwest China. This study aims to reveal the genetic process of the Beisantai deposit and constrain the mineralization characteristics conducted through petrographic observation, Rock-Eval pyrolysis, high-resolution microscopic mineralogical observation based on BSE, C-O isotopes of calcite cement, and in-situ measurements on pyrite of trace elements and S isotope. There are two types of calcite cements, including diagenetic microcrystalline calcite and epigenetic sparry calcite, dominantly occurring in the redox transition zone and the oxidation zone, respectively. The broad heterogeneity of δ13C values, ranging from −29.2‰ to −6.52‰, indicates the mixed sources of carbon. Given the poor organic content in sediments (0.05% in sandstone and from 0.11% to 0.26% in mudstones), the large amount of organic carbon in the transition zone conglomerates, revealed by the super low δ13C values, is attributed to extrinsic hydrocarbons. Besides, the widespread dissolution of microcrystalline calcite also indicates a weakly acidic environment in the formation. The heavy carbon isotopes are sourced from surface freshwater and the dissolved CO2, which causes the epigenetic metasomatism of early-stage calcite. Thus, the infiltrated groundwater is characterized as alkaline with carbonate dissolved. Pyrites are highly enriched in ore-bearing rocks, with complex morphologies. The extremely negative sulfur isotopic signatures (δ34S values from −48.38‰ to −35.65‰) indicate that these pyrites precipitate through bacterial sulfate reduction (BSR). Combined with the morphology features, distribution patterns, and the decrease in light sulfur isotope and several trace elements, including As, Se, Ni, and Co between individual pyrites and ore-related pyrites, a successive process of pyritization can be revealed. Ore-related pyrites are formed at the late stage. The pervasive coffinite replacement of pyrite suggests that uranium mineralization should occur after the cessation of pyritization, resulting from the consumption of organic matter. Distinctive bio-oxidation features of pyrite can also be observed, characterized as deep and oriented holes. Thus the role of microbes such as Acidithiobacillus thiooxidans is non-negligible, which enhances the dissolution rate of pyrite and the reduction of U(Ⅵ). Overall, as the major reducing material during the ore stage, the large amount of pyrite has played the predominant role in the precipitation of coffinite, with the catalysis and acceleration of microbes.