Accurate identification of the lithofacies and sedimentary facies of coal-bearing series is significant in the study of peat accumulation, coal thickness variation and coal-measured unconventional gas. This research integrated core, logging and 3D seismic data to conduct a comprehensive seismic–geological study on the sedimentary evolution characteristics and peat accumulation regularity of the Shanxi Formation in the Xinjing mining area of the Qinshui Basin. Firstly, the high-resolution sequence interface was identified, and the isochronous stratigraphic framework of the coal-bearing series was constructed. Then, the temporal and spatial evolution of sedimentary filling and sedimentary facies was dynamically analyzed using waveform clustering, phase rotation, stratal slice and frequency–division amplitude fusion methods. The results show that the Shanxi Formation in the study area can be divided into one third-order sequence and two fourth-order sequences. It developed a river-dominated deltaic system, mainly with delta plain deposits, and underwent a constructive–abandoned–constructive development stage. The locally distributed No. 6 coal seam was formed in a backswamp environment with distribution constrained by the distributary channels. The delta was abandoned at the later stage of the SS1 sequence, and the peat accumulation rate was balanced with the growth rate of the accommodation, forming a large-area distributed No. 3 thick coal seam. During the formation of the SS2 sequence, the No. 3 coal seam was locally thinned by epigenetic erosion of the river, and the thin coal belt caused by erosion is controlled by the location of the distributary channels and their extension direction. This study can provide a reference for the research on the distribution of thin sand bodies, sedimentary evolution and peat accumulation regularity in the coal-bearing series under the marine–continental transitional environment.