Abstract: The northern margin of the Qaidam Basin (NQB) preserves key records of the Mesozoic–Cenozoic tectonic evolution of the northeastern Tibetan Plateau. However, significant controversies remain regarding the nature of the Mesozoic basin (extensional vs. compressional) and the tectonic setting during the Paleogene. To address these issues, this study conducts detailed interpretation of two-dimensional and three-dimensional seismic data in the central segment of the NQB, yielding the following results. Integrating thermochronologic constraints, seismic reflection geometries, and regional analyses of fault activity, the structural succession of the area can be subdivided into three principal tectonic layers: the Mesozoic layer (Jurassic–Cretaceous), the Paleogene layer (Lulehe Formation (E₁₊₂) to the upper part of the Lower Ganchaigou Formation (E₃²)), and the Neogene-Quaternary layer (Upper Ganchaigou Formation (N₁) to Quaternary). Fault assemblages differ markedly among the tectonic layers. The Mesozoic layer is characterized by small-scale planar or listric normal faults; the Paleogene layer exhibits NW-trending imbricate thrust systems; and the Neogene-Quaternary layer is dominated by NW-trending thrust-related imbricate structures together with near-E-W-trending Y-shaped thrust-strike-slip faults. Based on the fault architecture within each tectonic layer, the tectonic evolution along the northern Qaidam Basin margin since the Mesozoic can be categorized into three major stages: a Mesozoic rifting phase (Late Triassic-Cretaceous), a Paleogene weak compressional phase (27-18 Ma), and a Neogene-Quaternary intense transpressional phase (5.1-2.8 Ma). This study clarifies the fault assemblage styles and their temporal evolution within different tectonic layers in the central segment of the northern Qaidam margin, providing new seismic evidence to constrain debates on the Mesozoic basin nature and Paleogene tectonic background of the northern Qaidam Basin. The identification of tectonic layering and stage-dependent intensification of compression and transpression also offers key constraints on basin–mountain coupled deformation mechanisms associated with the northward expansion of the northeastern Tibetan Plateau during the Cenozoic, and provides a valuable tectonic framework for structural analysis and resource exploration in the northern Qaidam margin.