Abstract The Choyr Basin is one of several Early Cretaceous rift basins in southwestern Mongolia that developed in specific regions between north–south trending fold-and-thrust belts. The eastern margin of the basin is defined by high-angle normal and/or strike-slip faults that trend north-to-south and northeast-to-southwest and by the overall geometry of the basin, which is interpreted to be a half graben. The sedimentary succession of the Choyr Basin documents one of the various types of tectono-sedimentary processes that were active in the rift basins of East Asia during Early Cretaceous time. The sedimentary infill of the Choyr Basin is newly defined as the Khalzan Uul and Khuren Dukh formations based on detailed mapping of lateral and vertical variations in component lithofacies assemblages. These two formations are heterotopic deposits and constitute a third-order fluvio-lacustrine sequence that can be divided into transgressive and highstand systems tracts. The lower part of the transgressive systems tract (TST) is characterized by sandy alluvial-fan and braided-river systems on the hanging wall along the western basin margin, and by a gravelly alluvial-fan system on the footwall along the eastern basin margin. The alluvial-fan and braided-river deposits along the western basin margin are fossiliferous and are interpreted to have developed in association with a perennial fluvial system. In contrast, alluvial-fan deposits along the eastern basin margin do not contain any distinct faunas or floras and are interpreted to have been influenced by a high-discharge ephemeral fluvial system associated with fluctuations in wetting and drying paleohydrologic processes. The lower part of the TST deposit fines upward to siltstone-dominated flood-plain and ephemeral-lake deposits that constitute the upper part of the TST and the lower part of the highstand systems tract (HST). These mudstone deposits eventually reduced the topographic irregularities typical of the early stage of synrift basin development, with an associated decrease in topographic-slope gradients. Finally, a high-sinuosity meandering river system drained to the south during the late highstand stage in response to the northward migration of the depocenter. The upper HST deposits are also fossiliferous and are interpreted to have been influenced by a perennial fluvial system, although the average annual discharge of this system was probably less than 5 percent of that involved in the formation of the lower TST deposits along the western basin margin.