The Sichuan-Yunnan region in southwest China is located in the boundary area between the active Tibetan Plateau to the west and the stable South China platform to the east. This region is characterized by complex Cenozoic structures and active seismotectonics. In this study, we have used over 30,000 arrival times from 1315 local earthquakes recorded by 172 seismic stations to determine a detailed three-dimensional (3-D) P wave velocity structure of the lithosphere down to 85 km depth in this region. We have taken into account the complex morphology of the Moho discontinuity to conduct the tomographic inversions, which leads to a better result than that with a flat Moho as in the previous studies. Our results show that large velocity variations of up to 7% exist in the crust and upper mantle in the Sichuan-Yunnan region. The velocity image of the upper crust correlates with the surface geological features. The Sichuan basin is imaged as a prominent low-velocity zone, while the Panzhihua mining district is imaged as a high-velocity feature. Velocity changes are visible across some of the large fault zones, and the faults and some large crustal earthquakes seem to occur at the boundary areas between slow and fast velocity anomalies. Some of the faults, such as the Red River fault, may have cut through the crust and reached up to the upper mantle. Under the Tengchong volcanic area, strong low-velocity zones are visible down to 85 km depth, with a lateral extent of about 100 km, suggesting the existence of magma chambers under the volcano. It is unclear how the Tengchong intraplate volcanism was generated. It may be related to the collision processes between the Indian plate, Burma microplate and the Eurasian plate, and the possible subduction of the Burma microplate under the Eurasian plate. Another possibility is that it was caused by the extensional fractures of the lithosphere and the upward intrusion of the hot asthenospheric materials. It is also possible that the Tengchong volcanism represents a hot spot with a lower mantle origin.