The special seismic tectonic environment and frequent seismicity in the southeastern margin of the Qinghai–Tibet Plateau show that this area is an ideal location to study the present tectonic movement and background of strong earthquakes in mainland China and to predict future strong earthquake risk zones. Studies of the structural environment and physical characteristics of the deep structure in this area are helpful to explore deep dynamic effects and deformation field characteristics, to strengthen our understanding of the roles of anisotropy and tectonic deformation and to study the deep tectonic background of the seismic origin of the block’s interior. In this paper, the three-dimensional (3D) P-wave velocity structure of the crust and upper mantle under the southeastern margin of the Qinghai–Tibet Plateau is obtained via observational data from 224 permanent seismic stations in the regional digital seismic network of Yunnan and Sichuan Provinces and from 356 mobile China seismic arrays in the southern section of the north–south seismic belt using a joint inversion method of the regional earthquake and teleseismic data. The results indicate that the spatial distribution of the P-wave velocity anomalies in the shallow upper crust is closely related to the surface geological structure, terrain and lithology. Baoxing and Kangding, with their basic volcanic rocks and volcanic clastic rocks, present obvious high-velocity anomalies. The Chengdu Basin shows low-velocity anomalies associated with the Quaternary sediments. The Xichang Mesozoic Basin and the Butuo Basin are characterised by low-velocity anomalies related to very thick sedimentary layers. The upper and middle crust beneath the Chuan–Dian and Songpan–Ganzi Blocks has apparent lateral heterogeneities, including low-velocity zones of different sizes. There is a large range of low-velocity layers in the Songpan–Ganzi Block and the sub–block northwest of Sichuan Province, showing that the middle and lower crust is relatively weak. The Sichuan Basin, which is located in the western margin of the Yangtze platform, shows high-velocity characteristics. The results also reveal that there are continuous low-velocity layer distributions in the middle and lower crust of the Daliangshan Block and that the distribution direction of the low-velocity anomaly is nearly SN, which is consistent with the trend of the Daliangshan fault. The existence of the low-velocity layer in the crust also provides a deep source for the deep dynamic deformation and seismic activity of the Daliangshan Block and its boundary faults. The results of the 3D P-wave velocity structure show that an anomalous distribution of high-density, strong-magnetic and high-wave velocity exists inside the crust in the Panxi region. This is likely related to late Paleozoic mantle plume activity that led to a large number of mafic and ultra-mafic intrusions into the crust. In the crustal doming process, the massive intrusion of mantle-derived material enhanced the mechanical strength of the crustal medium. The P-wave velocity structure also revealed that the upper mantle contains a low-velocity layer at a depth of 80–120 km in the Panxi region. The existence of deep faults in the Panxi region, which provide conditions for transporting mantle thermal material into the crust, is the deep tectonic background for the area’s strong earthquake activity.