The gold mineralization in the Mianlue belt, western Qinling Mountains, has been a hotspot in geoscience research in recent years. In particular, important breakthroughs have been achieved in terms of prospecting in the medium-sized Shuidegou gold deposit, located in the middle of the Mianlue belt. Here, we present the results of systematic tectonic and chronological analyses conducted on the Shuidegou gold deposit. The reconstructed zircon U–Pb chronologies of the ore-bearing altered rocks and of the ore-bearing vein demonstrated that the Shuidegou gold deposit formed at ~183 Ma and was further enriched at ~ 150 Ma. The macro- and micro-structures identified in deformed geologic bodies and quartz c-axis fabrics in the mining area suggest a division of the deformation sequence into four phases, corresponding to: (1) a Mid–Late Triassic collision and convergence of middle–deep deformation structures during the main orogenic period (D1); (2) a Late Triassic–Early Jurassic collision and convergence during the late-stage thrust-nappe tectonic deformation (D2); (3) a Mid–Late Mesozoic shallow strike-slip shear structure stage during intracontinental orogeny (D3); (4) post-Cretaceous, shallow brittle thrust extrusion strike-slip structure (D4). Based on the deformation and zircon U–Pb chronological features of the Shuidegou gold deposit, we believe that the main metallogenic age (~183 Ma) corresponds to the thrust-shear deformation stage (D2) and that it is genetically connected with magmatism. Notably, the late-stage further enrichment(~150 Ma) occurred in the sinistral strike-slip stage. Ore-bearing fluids may have been restricted by the far-field effect of the Pacific plate subduction along the eastern edge of East Asia. Based on the macro- and micro-deformation features, the chronological data relative to the key geologic bodies, and the regional geologic background, we subdivided the mineralizing process of the Shuidegou gold deposit is composed into three stages: (1) the formation of an ore-guiding channel, (2) the deposition and mineralization of ore-forming elements, and (3) a later further enrichment. The study of ore-controlling structure showed that the development of the Shuidegou gold deposit was mainly controlled by WNW- (E–W) and NNE-trending structures during the two metallogenic periods (~183 Ma and ~ 150 Ma, respectively). Concerning this aspect, the Shuidegou gold deposit contrasts with some typical gold deposits in the same region.