The southeastern margin of the Tibetan Plateau (SETP) presents the highest level of seismicity in mainland China. To understand the seismicity in this region, a new seismic experiment is carried out based on the tomographic inversion of P- and S-wave arrival times from the regional earthquakes recorded by 49 seismic stations in Yunnan Province of Southwest China. In this study, we reduce the extreme disproportionality of the data distribution using an events combination method, and we use arrival times to construct the reference velocity model. Checkerboard tests and odd/even data tests are carried out to assess the reliability of the inversion results. The reliable P-wave velocity model reveals two low-velocity anomaly zones (LVAZs) bounded by major strike-slip faults. Almost all the large earthquakes in this region occurred in the two LVAZs and the trend of the two LVAZs is consistent with a global positioning system velocity field based on the Eurasia-fixed reference frame. We propose that the two LVAZs are material migration passageways in the SETP. In the vertical direction, the mechanically weak crustal materials are sliding southward with the rigid block, while the underlying mantle materials continue to be compressed by the collision. This vertical model is broadly consistent with the seismic anisotropy in the crust and lithospheric mantle from shear-wave splitting. The new regional geodynamic model gives a reasonable interpretation of the seismicity of the SETP, and we suggest that the material migration in the passageway zones plays an important role in the tectonic evolution of the SETP.