The Bohai Bay Basin is a Mesozoic subsidence and Cenozoic rift basin in the North China Craton. Since the deposition of the Permo-Carboniferous hydrocarbon source rock, the basin has undergone many tectonic events. The source rocks have undergone non-uniform uplift, twisting, deep burying, and magmatism and that led to an interrupted or stepwise during the evolution of hydrocarbon source rocks. We have investigated the Permo-Carboniferous hydrocarbon source rocks history of burying, heating, and hydrocarbon generation, not only on the basis of tectonic disturbance and deeply buried but also with new studies on apatite fission track analysis, fluid inclusion measurements, and the application of the numerical simulation of EASY%Ro. The heating temperature of the source rocks continued to rise from the Indosinian to Himalayan stage and reached a maximum at the Late Himalayan. This led to the stepwise increases during organic maturation and multiple stages of hydrocarbon generation. The study delineated the tectonic stages, the intensity of hydrocarbon generation and spatial and temporal distribution of hydrocarbon generations. The hydrocarbon generation occurred during the Indosinian, Yanshanian, and particularly Late Himalayan. The hydrocarbon generation during the late Himalayan stage is the most important one for the Permo-Carboniferous source rocks of the Bohai Bay Basin in China.