The relationship between uranium mineralisation and sedimentary facies in a fluvial depositional setting remains a challenging topic. However, the specific effect of muti-scale sedimentary facies control on meandering sandstone-type uranium enrichment is poorly understood. Based on sedimentological, geochemical, mineralogical, and petrophysical analyses, three third-order sequences (SQ1, SQ2, and SQ3) composed of four systems tracts in meandering deposits were identified in the Sifangtai Formation of the northern Songliao Basin. Four subfacies (channel, levee, flood, and abandoned channels) and seven microfacies were identified in meandering rivers, exhibiting spatio-temporal migration of sedimentary fillings. Here, uranium deposits were mainly enriched in semi-abandoned channel deposits during the lowstand systems tract (LST) period of SQ1. Stable-distributed and thick-layered industrial-grade uranium deposits occurred in a positive rhythmic rock assemblages, exhibiting high-frequency variation from thicker medium–fine sandstone to thin charcoal-rich siltstone–fine sandstone. Rapid tectonic uplift and warm-semi humid climate during early Sifangtai period controlled sequence growth and sedimentary filling. Furthermore, sequence and sedimentation during the LST period mediated the formation of uranium-rich rock assemblage and fluid migration pathway, reacting on the abundance, location, and distribution of uranium enrichment. Ultimately, a conceptual model of the sequence and sedimentary control on uranium accumulation was established in the context of meandering rivers. This model revealed that semi humid-warm climate and tectonic inversion (74.9–72.2 Ma) control meandering river, sedimentary hiatus, and charcoal-rich uranium-hosted rock series formation in the LST. Enhanced Cenozoic tectonic uplift (38.0–10.0 Ma) and continental weathering prompted uranium-rich fluids along steep paleotopography, migrated to geochemical barriers of charcoal-rich rock series, and reductive mineralisation around semi-abandoned channel deposits. Our results illustrate the importance of examining multi-scale sedimentary facies to interpret the uranium accumulation process of meandering deposits, ultimately contributing to uranium exploration in similar settings.