The Ordos Basin contains abundant coal resources in the Upper Paleozoic strata. They are shallowly buried or exposed in the periphery of the basin, forming recoverable coal mines and coalbed methane resources. For the deeply buried coal seams of the basin, however, due to complex changes and difficult mining, less attention was paid before. In recent years, with the exploitation of tight gas related to coal source rocks, a large amount of drilling and seismic data has been accumulated in the southeastern Ordos Basin, which makes it possible to study the distribution change and factors controlling Upper Paleozoic coal seams. Delineation of deep coal development and distribution is an important basis for coal, coalbed methane and related tight gas resources in the Upper Paleozoic. We use core, logging and seismic data to analyze the coal geophysics, thickness variation, paleotopography and sedimentary facies in the southeastern Ordos Basin. The lower part of the Shanxi Formation (Fm.) and the upper part of the Taiyuan Fm. in the southeastern part of the basin are characterized by low natural gamma ray, low density, high resistivity and high sonic logging values. As the coal velocity is very low and alternates with the high-velocity Taiyuan Fm. and Ordovician limestones, the two sets of coals below and above the Taiyuan limestones form an extremely strong-amplitude reflection in the seismic profile. The two sets of coals are cumulatively 1–10 m thick, averaging 2.4 m, and 4 m is the maximum induvial thickness. The individual coal seams thicker than 2 m cover an area of approximately 2500 km2, and the burial depths of the coal seam range from 2500 to 3000 m. The thick coal seams of the Taiyuan Fm. are mainly distributed proximally in the Ordovician paleokarst depression, while the Ordovician paleokarst depression without incised origin was deposited by distal coeval limestone rocks. There is a complementary relationship between the coal seams and the thickened zone of distributary channel sandstone in the Shanxi Fm.