Lacustrine organic-rich Eocene shales are well developed within the faulted lake basin in the Bohai Bay Basin in eastern China. It is crucial to comprehend the sedimentation of these shales for the study of depositional processes, paleoenvironment reconstruction, and shale oil exploration. This research investigates the sedimentary characteristics and formation mechanisms of lacustrine shales in the upper fourth member and lower third member of the Eocene Shahejie Formation (Es4s–Es3x shale), based on thin sections and field-emission scanning electron microscopy observations of well cores, with x-ray diffraction analysis, electron probe microanalysis, and geochemical elements analysis. The Es4s–Es3x shale is deposited in a hypoxic saline lake with laminated, massive, and lenticular sedimentary structures, wherein laminated shale is the dominant lithofacies. Eight laminae units have been identified: micritic calcite laminae (MCAL), sparry calcite laminae (SCAL), quartz–feldspar–clay mixed laminae (QFCL), organic-rich clay laminae (OCL), clay laminae (CL), organic matter laminae (OL), dolomite laminae (DL), and anhydrite laminae (AL). They form seven lamina couplets: MCAL + OL + CL, QFCL + OCL, SCAL + OCL, SCAL + OL, MCAL + QFCL, DL + OCL, and DL + AL. Moreover, three massive lithofacies have been identified: massive siltstone and claystone, massive limestone/silty limestone, and massive dolomite. Three calcite lenticular laminae have also been identified. The Sr/Ba, S/total organic carbon, and Th/U ratios and other geochemical elements show that Es4s–Es3x shale is deposited in the hypoxic saline lake. Factors such as lake water, salinity, oxidation reduction, and water depth all vary with episodic high frequency. The lithology, lithofacies sequence, and geochemical characteristics denote that the laminated shale was deposited via suspension. The halocline in the lake is a key factor controlling the lacustrine laminae deposition and the lamina couplet distribution in the lake basin. The halocline location fluctuations are controlled by the dynamic equilibrium of the water depth and terrigenous input, which further control the development of different laminae and lamina couplets. Massive mudstone formed due to turbidity, debris flows, and evaporation. The MCAL may have been deposited due to breakdown and resuspension under strong hydrodynamics. Additionally, erosion, deposition, and compaction of water-rich muds and biodisturbance control the formation of the three lenses.