The Boxing Sag is located in the southwest of Dongying Depression, southern Bohai Bay Basin of East China. It is one of the main petroliferous sags in the Dongying Depression, and has two major source rocks, namely the upper 4th Member (Es4u) and lower 3rd Member (Es3l) shales of Eocene Shahejie Formation, which are the new exploration targets in recent years. In this study, 16 core samples were collected from Es4u and Es3l shales in the Boxing Sag, and the saturate hydrocarbons were analyzed by gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS), respectively. The results show that Es4u shale has obvious phytane and gammacerane predominance, higher concentration of tricyclic terpanes and regular steranes, and very low concentration of 4-methly steranes; Es3l shale has pristane predominance, lower concentration of tricyclic terpanes, gammacerane and regular steranes, and higher concentration of 4-methly steranes. The Es4u shale can be further divided into two types based on the distribution of n-alkanes in gas chromatograms: normal distribution and double peak pattern. The biomarker characteristics and sedimentary facies distribution show that Es4u shale was deposited in the saline-hypersaline semi-deep (Type A Es4u shale, sag center) to shallow (Type B Es4u shale, sag edge) lacustrine environments, Es3l shale was deposited in the freshwater-brackish semi-deep-deep lacustrine environments, and the former sedimentary facies maps of Es4u and Es3l in the Boxing Sag are further modified.