The Lower Paleozoic of the Awati Sag and its periphery is a region with relatively low levels of exploration and stands as a frontier for ultra-deep hydrocarbon exploration. Based on outcrop and core samples, this study integrated organic geochemical analysis, total organic carbon (TOC) logging interpretation, and one-dimensional and two-dimensional hydrocarbon accumulation simulations, to clarify the primary source rock of the Lower Paleozoic and its characteristics, as well as its hydrocarbon accumulation mode. The findings indicate the following: (1) The Lower Paleozoic features two sets of industrial source rocks. The Yuertusi Formation, with its considerable thickness (approximately 200 m), widespread distribution, and elevated TOC (averaging approximately 5% from experimental data and logging interpretation), stands out as the Lower Paleozoic’s most pivotal source rock. (2) The Yuertusi and Saergan Formations are in a high-to-over-mature stage, with the Yuertusi initiating oil generation in the early Silurian and transitioning to gas by the late Permian. The Saergan began producing oil in the Carboniferous, followed by gas in the late Permian. (3) The potential ultra-deep gas reservoirs in the Awati Sag are mainly distributed in the structural traps closer to the deep faults in five potential target formations. Deep natural gas typically exhibits mixed-source signatures, with the mixing notably pronounced along the Shajingzi Fault Belt due to influential basin-controlling faults.