Organic-rich continental and marine–continental (i.e., transitional) shales are characterized by numerous hydrocarbon production layers having an uneven horizontal distribution, which are challenging to locate and exploit. We examined the effects of karst topography on organic carbon accumulation during the early Permian in the southeastern Ordos Basin, northwestern China, using outcrop and well data. Our study involved geomorphological, sedimentological, petrological, and geochemical methods. We identified a regional unconformity on the Dongdayao Limestone (DDYL) that formed in the early Permian (Asselian; i.e., in the Shanxi Formation) in the study area based on (1) cave, pore, and breccia development in outcrops and drill cores; (2) high Mn–Fe and low Sr contents associated with negative δ18O and normal δ13C values, which are indicative of strong leaching by meteoric waters; and (3) the irregular thickness of the DDYL that is indicative of differential karstification, resulting in the formation of horizontal gullies. The karst topography of the DDYL was identified based on the moldic and residual thickness methods, including karst highland, gentle slope, and microbasin geomorphic units. We propose that the karst topography controlled the redox environment and led to enrichment of the organic-rich transitional shales in the selected submember of the Shanxi Formation. The U/Th, V/Cr, and V/(V+Ni) ratios exhibit a linear relationship with geomorphic unit types. The karst microbasins had a weakly oxic environment, which widely preserved thick, organic-rich, transitional shales having high total organic carbon content and gas-bearing potential.