Abstract: The geological conditions for natural gas accumulation in the deep subsalt layers of the second and third members of the Ordovician Majiagou Formation (Ma 2 and Ma 3) in the Ordos Basin are complex, and favorable exploration directions in this area remain unclear. These disadvantages result in a lack of major breakthroughs in subsalt exploration. To clarify the geological characteristics of deep subsalt natural gas accumulation and to identify new exploration potential zones, a systematic analysis of the geological conditions was conducted using drilling, seismic, logging, and analytical testing data. The geological causes for poor gas testing performance in subsalt layers were revealed, and favorable exploration directions and accumulation models for deep subsalt natural gas were proposed. The results indicated that source rocks, reservoirs, and faults were the main factors controlling the distribution of deep subsalt natural gas. The Ma 2 and Ma 3 members in the deep subsalt layers exhibited spatial differences in hydrocarbon supply characteristics. In the eastern part of the basin, the hydrocarbon supply was mainly derived from Lower Paleozoic marine oil-type gas, with a relatively higher carbon isotope value in methane (-41.6‰). In the central part of the basin, the supply was a mixture of Lower Paleozoic marine oil-type gas and Upper Paleozoic coal-derived gas, with moderate amounts of carbon isotope in methane (-35.9‰). On the eastern side of the central paleo-uplift, the basin could be further divided into the northwestern and southwestern parts. In the northwestern part, the hydrocarbon supply was a mixture of Lower Paleozoic oil-type gas and Upper Paleozoic coal-derived gas, with an intermediate carbon isotope value in methane (-38.7‰). In the southwestern part, the supply was primarily from Upper Paleozoic coal-derived gas, with a significantly higher carbon isotope value in methane (-32.2‰). The deep subsalt reservoirs are diverse in types, mainly controlled by paleo-geomorphology and sedimentary facies zones, with evident zoning characteristics. High-quality reservoirs mainly develop gypsum mold pores, caves, and shoal pores. The role of faults in facilitating the migration and conduction of subsalt natural gas is relatively limited. The widely developed gypsum salt layers in Ma 2 and Ma 3 members exhibit strong plasticity and are prone to deformation, which to some extent obstructed and reduced the vertical and lateral migration capacity of natural gas. This resulted in the overall low abundance of deep subsalt natural gas. Based on the comprehensive analysis, three favorable exploration directions were proposed: lateral hydrocarbon supply on the eastern side of the central paleo-uplift, self-generated and self-stored reservoirs in the eastern basin, and effective source, reservoir and fault matching zones in the central basin. Corresponding accumulation models were established.