Karstification in carbonate successions has an important influence on hydrocarbon accumulation. Taking the Ordos Basin, currently the largest petroliferous basin in China, as an example, this study examines the large‐scale, long‐term (~120 Myr) paleokarst at the top of the Ordovician. The objectives of the study are to characterize the karst paleogeomorphology of this area, to explain the inconsistency between existing understandings of karst paleogeomorphology and exploration in the eastern Ordos Basin, and to reveal the control of paleokarst on natural gas accumulation and its paleogeographic significance. A total of 860 exploration wells were used for detailed stratigraphic correlation and analysis, along with core observations, well‐logging analyses, physical property characterization, and isotope analyses. Results of residual thickness and moldic thickness reconstruction reveal variation in karst paleogeomorphology between north and south in the eastern Ordos Basin, differing from the traditionally recognized E‐W variation. Two geomorphic units are classified as follows: the karst highland and the karst slope from north to south, with the karst slope being subdivided into northern and southern slope areas. The karst highland area has negligible reservoir capacity and hydrocarbon accumulation owing to the enhanced denudation that occurred there. In contrast, the northern karst slope shows favorable reservoir properties and has abundant gas wells according to well‐logging interpretations, whereas the southern karst slope is of poor reservoir quality and hosts mainly water wells. Differences in dissolution‐filling effects controlled by the surface paleodrainage system are suggested to be the main contributor to differential reservoir space preservation, which, together with the variable width and depth of source rocks in the grooves (thereby variably exposing source rock), further promoted differential gas accumulation. The Ordos Basin and its periphery in the southwestern North China Craton (NCC) show inheritance of sedimentary‐tectonic patterns from the Middle Ordovician to the Late Carboniferous. These results should provide a reference for hydrocarbon exploration in the Ordovician of other basins in the NCC in which karst occurs and karst basins worldwide, and deepens understanding of the paleogeographic framework in the context of regional uplift of the North China Platform.