Carbonate weathering crust reservoirs have consistently represented a pivotal area of research in hydrocarbon exploitation. Karst paleogeomorphology emerges from the intricate interplay of weathering, denudation, karstification, and diverse geological conditions. Various landforms significantly influence the distribution of karst reservoirs; thus, reconstructing paleogeomorphology establishes an essential foundation for subsequent investigations into carbonate reservoirs and gas reservoir distributions. A pertinent example is found in the Yan’an area of China, where the paleogeomorphology of the Ordovician Majiagou Formation remains inadequately understood. Based on the sedimentary background and reservoir characteristics, the impression method, residual thickness method and trend surface compensation method are adopted to collaboratively restore the Ordovician paleogeomorphology to elucidate how different landform units affect gas reservoir distribution. The findings indicate that the study area’s paleogeomorphology consists of a karst highland in the west, a karst slope in the central, and a karst basin in the east. The paleotopography reveals a tectonic configuration characterized by a steep terrain in the west transitioning to gentler slopes in the east. Additionally, eight third-order paleogeomorphic units were delineated within these second-order units: upland, tableland, hillside, valley, gentle hill, terrace, monadnock, and depression, respectively. Due to various geological processes like denudation and leaching, the influences on physical properties vary markedly across geomorphic units. Notably favorable natural gas accumulation zones include gentle hills on the karst slope, as well as monadnocks within the karst basin alongside both sides of valleys exhibiting pronounced karstification with excellent reservoir qualities. This study may be applied to basins with similar sedimentary backgrounds, by analogy, to more systematically reconstruct the paleogeomorphology and predict the favorable areas for gas accumulation.