The Bohai Sea area is a complex lacustrine rift basin characterized by multistage rifts, polycycle superimpositions, and multiple genetic mechanisms. We recognized three types of sequence boundaries from the Paleogene strata of offshore Bohai, including 2 first-, 3 second-, and 10 third-order sequence boundaries. The third-order wedges, composed of the low-stand system tract (LST), lake expansion system tract (EST), and high-stand system tract (HST), are significant for hydrocarbon exploration. The sequence stratigraphic patterns vary in different periods. We discovered that the LST and EST are mainly developed in the rifting stage, whereas the HST is developed in the subsidence stage. Sequences developed in different depressions present significant variations, but the migration of the depocenter from the margin to the center during basin evolution can still be clearly recognized. Vertically, episodic tectonism plays an important role in controlling the formation of sequence boundaries, sequence structural features, and sequence architectural patterns. However, various rift basin marginal tectonics control the lateral sequence architectures. Because each structure belt is characterized by a unique sequence framework due to the strong influence of basin rifting processes, we establish a corresponding sequence stratigraphic model for the specific tectonic environment using process-based sequence stratigraphic methods.