The North Yellow Sea Basin (NYSB) is one of the petroliferous basins in the offshore region of eastern China. An integrated sequence stratigraphic–geochemical investigation was carried out to identify and assess the effective source rocks of recent oil discoveries in the NYSB. A total of four third-order sequences (the first [J₂SQ1] and second [J₂SQ2] third-order sequence within the Middle Jurassic, and the first [J₃SQ1] and second [J₃SQ2] third-order sequence within the Upper Jurassic) were identified in the Jurassic succession, in which four types of probable source rocks were distinguished, namely, lacustrine deep-water mudstones, lacustrine shallow-water mudstones, prodeltaic mudstones, and deltaic-plain mudstones. The lacustrine deep-water mudstones are widely distributed within the J₂SQ1, J₂SQ2, and J₃SQ2 sequences in the gentle tectonic slope and depression area. They are characterized by moderate total organic carbon (TOC) contents (0.79−3.72 wt. %, with an average of 1.71 wt. %), lower hydrocarbon potential indexes (the amount of free hydrocarbons before analysis [S₁] and the amount of hydrocarbons that results from cracking of kerogen [S₂], i.e., S₁+ S₂, in a sample during Rock-Eval pyrolysis) (0.97 mg HC/g rock < S₁ + S₂ < 7.89 mg HC/g rock, with an average of 3.10 mg HC/g rock), and predominantly type II to type III kerogen. In contrast, the prodeltaic mudstones in J₃SQ2 have higher TOC contents (1.5−4.0 wt. %, with an average of 2.71 wt. %), higher S₁ + S₂ (5.83−25.51 mg HC/g rock, with an average of 14.89 mg HC/g rock), and predominantly type I to type II kerogen. The oil–source correlation results indicate that the oils discovered in the NYSB mainly originated from the prodeltaic J₃SQ2 mudstones. The effective source kitchen is mainly located in the northwestern part of the study area. The factors controlling the occurrence of high-quality prodeltaic source rocks are a sufficient supply of nutrients and terrigenous organic matter, high depositional rates, and a suboxic environment.