The structural characteristics and evolution history of the eastern margin of Pamir are of great significance to reveal the deformation and evolution of the western syntaxis of the Tibetan Plateau, the basin-mountain coupling relationship between the Pamir–West Kunlun and the Tarim Basin, and to guide the exploration of oil and gas resources and earthquake disaster prevention in this region. Based on the detailed surface mapping and structural analysis of seismic profiles across key locations, the tectonic framework of the basin-range junction zone in the eastern margin of the Pamir is constrained. The mapping data, field photos, seismic profiles and other data presented in this paper reveal that a dextral strike-slip fault system outcrops in the eastern margin of the Pamir, and a buried compressional thrust belt develops in the adjacent basin, including the Qipan structural wedge and the Qimugen structural wedge. The growth strata of the Qipan structural wedge is located in the lower section of the Pliocene Artux Formation, while the growth strata of the Qimugen structural wedge is located at the top of the Pliocene Artux Formation, indicating that the thrust belt has been developed since the Pliocene. The eastern margin of the Pamir experienced a tectonic transformation from a strike-slip tectonic system to a compressional tectonic system during the Pliocene. Before the Pliocene, deformation was accommodated by dextral strike-slip of the Wuyitake-Momoke transfer system (WMTS); Since the Pliocene, deformation in this area was dominated by eastward thrusting, and the strike-slip activity decreased. These basic data and the basic viewpoints put forward in this paper have a good guiding significance for establishment of the tectonic framework and evolution sequence of this region.