In this study, we compiled and analyzed 69310 P-wave travel-time data from 6639 earthquake events. These events (M ≥ 2.0) occurred from 1980s to June 2019 and were recorded at 319 seismic stations (Chinese Earthquake Networks Center) in the study area. We adopted the double-difference seismic tomographic method (tomoDD) to invert the 3-D P-wave velocity structure and constrain the crust-upper mantle architecture of the Middle and Lower Reaches of the Yangtze River Metallogenic Belt (MLYB). A 1-D initial model extracted from wide-angle seismic profiles was used in the seismic tomography, which greatly reduced the inversion residual. Our results indicate that reliable velocity structure of the uppermost mantle can be obtained when Pn is involved in the tomography. Our results show that: (1) the pattern of the uppermost mantle velocity structure corresponds well with the geological partitioning: a nearly E–W-trending low-velocity zone is present beneath the Dabie Orogen, in contrast to the mainly NE-trending low-velocity anomalies beneath the Jiangnan Orogen. They suggest the presence of thickened lower crust beneath the orogens in the study area. In contrast, the Yangtze and Cathaysia blocks are characterized by relatively high-velocity anomalies; (2) both the ultra-high-pressure (UHP) metamorphic rocks in the Dabie Orogen and the low-pressure metamorphic rocks in the Zhangbaling dome are characterized by high-velocity anomalies. The upper crust in the Dabie Orogen is characterized by a low-velocity belt, sandwiched between two high velocity zones in a horizontal?direction, with discontinuous low-velocity layers in the middle crust. The keel of the Dabie Orogen is mainly preserved beneath its northern section. We infer that the lower crustal delamination may have mainly occurred in the southern Dabie Orogen, which caused the mantle upwelling responsible for the formation of the granitic magmas emplaced in the middle crust as the low-velocity layers observed there. Continuous deep-level compression likely squeezed the granitic magma upward to intrude the upper crustal UHP metamorphic rocks, forming the ‘sandwich’ velocity structure there; (3) high-velocity updoming is widespread in the crust-mantle transition zone beneath the MLYB. From the Anqing-Guichi ore field northeastward to the Luzong, Tongling, Ningwu and Ningzhen orefields, high-velocity anomalies in the crust-mantle transition zone increase rapidly in size and are widely distributed. The updoming also exists in the crust-mantle transition zone beneath the Jiurui and Edongnan orefields, but the high-velocity anomalies are mainly stellate distributed. The updoming high-velocity zone beneath the MLYB generally extends from the crust-mantle transition zone to the middle crust, different from the velocity structure in the upper crust. The upper crust beneath the Early Cretaceous extension-related Luzong and Ningwu volcanic basins is characterized by high velocity zones, in contrast to the low velocity anomalies beneath the Late Jurassic to Early Cretaceous compression-related Tongling ore field. The MLYB may have undergone a compressive-to-extensional transition during the Yanshanian (Jurassic–Cretaceous) period, during which extensive magmatism occurred. The near mantle–crustal boundary updoming was likely caused by asthenospheric underplating at the base of the lower crust. The magmas may have ascended through major crustal faults, undergoing AFC (assimilation and fractional crystallization) processes, became emplaced in the fault-bounded basins or Paleozoic sequences, eventually forming the many Cu-Fe polymetallic deposits there.