For nearly 60 years, petroleum geologists have been puzzled by oil and gas exploration in the South Yellow Sea basin, which is considered to have broad oil and gas prospects, but no commercial hydrocarbon reservoirs have been obtained. The hydrocarbon-bearing geological conditions of the Permian strata with good exploration prospects also have never been systematically investigated. To solve the problem, a series of experiments was conducted on core samples obtained from borehole CSDP-2, the first exploration well with continuous coring in the South Yellow Sea Basin, including petrology analysis, geochemical testing, pore-throat testing, hydrocarbon-charging analysis, and sealing-ability evaluation. Vitrinite reflectance (Ro), total organic carbon (TOC), pyrolysis, extractable organic matter (EOM) and kerogen microscopic examination were carried out to evaluate the quality of the Permian source rocks. Porosity, permeability, thin section, scanning electronic microscopy (SEM) and rate-controlled mercury injection (RCMI) analyses were combined to verify the effectiveness of sandstone reservoirs. The sealing capacity of caprock was mainly evaluated by the displacement pressure. And according to the fluid-inclusion analysis and oil-source correlation, the hydrocarbon accumulation events were determined. After comprehensive analysis, we clarified the effective hydrocarbon-bearing geological conditions and favorable prospects in the Permian of the South Yellow Sea Basin. Furthermore, the main controlling factors pertaining to favorable source rocks and tight sandstone reservoirs were ascertained in this paper.The results show that two sets of the Lower Permian Qixia and Gufeng Formation (P1q-g) and the Upper Permian Longtan and Dalong Formation (P2l-d) source rocks, along with the P2l-d tight sandstone reservoirs, compose two types of hydrocarbon accumulation assemblages, which are effectively sealed by the Lower Triassic Qinglong Formation (T1q) roof caprock. One type represents the ‘lower-generation and upper-accumulation’ between the P1q-g source rocks and the P2l-d sandstones, and the other type represents the ‘self-generation and self-accumulation’ in the Upper Permian strata. Vertical stacking between the Permian source rocks and sandstone reservoirs ensures the near-source hydrocarbon accumulation, and faults and microcracks can be regarded as beneficial channels for hydrocarbon migration. In addition, we find that the quality of source rocks is improved by large-scale marine transgression, high bio-productivity, and tectonic–thermal events. The quality of tight sandstone reservoirs is more dependent on throats with relatively larger radius than pores. This study provides important enlightenment for exploring marine hydrocarbons in the South Yellow Sea Basin, and can be useful in understanding the dominant geological factors affecting favorable source rocks and sandstone reservoirs.