Systematic organic petrology and geochemistry analyses have been conducted in the source rocks of the lower Es3 and upper Es4 members of the Shahejie Formation in the Niuzhuang Sub-sag, Jiyang Depression, Bohai Bay Basin, eastern China. The results indicate that the main organic types of shale and nongypsum mudstone in the lower Es3 and upper Es4 member are I-II1 kerogen, and the predominant () activation energy frequencies range from 57 to . The similar distribution characteristics in the two source rocks indicate that they have a similar hydrocarbon maturation process. An extensive pyrolysis analysis indicates that the source rocks of the upper Es4 member do not have an obvious double peak hydrocarbon generation model. Previous studies indicate that the hydrocarbon index peak at a depth of 2500–2700 m is affected by migrating hydrocarbon. Major differences are not observed in the hydrocarbon generation and evolution process of the shale and nongypsum mudstone. The primary oil generation threshold of the lower Es3 and upper Es4 members is approximately 3200 m, and the oil generation peak is approximately 3500 m. The activation energy distribution of the gypsum mudstone of the upper Es4 member is wider than that of the shale and nongypsum mudstone, and lower activation energies account for a larger proportion of the activation energies. The above factors may lead to a shallower oil generation threshold for gypsum mudstone compared with that for shale and nongypsum mudstone.