Southeastern Tibet is a key region for studying the tectonic evolution of Tibetan Plateau. The region is characterized by distributed faults, localized low-velocity zones (LVZs) in the mid-lower crust, and prominent clockwise rotation of GPS velocity field. End-member models have been proposed to explain the origin of this deformation pattern, including the block extrusion model highlighting the role of faulted shear zones, and the crustal flow model emphasizing the effect of a weak lower crust. Here we use a 3D visco-elasto-plastic finite element model to reproduce the instantaneous horizontal surface velocity and investigate the effects of active faults and LVZs on that. The results show that when only faults are included, the residual surface velocities between modeled and observed values are large at some locations overlying the LVZs; when only LVZs are included, the residual surface velocities along the Xianshuihe-Xiaojiang and Lijiang-Xiaojinhe faults, two major faults with relatively high slip rates, are significant. However, when both faults and LVZs are considered, the modeled surface velocities fit well with observed GPS velocities. Our results therefore demonstrate that a combination of fault-bounding block extrusion and crustal flow type of continuous deformation is required to explain the surface deformation. The model yields a high-resolution strain rate map which provides an improved understanding of Quaternary tectonics and seismic hazards. In order to reduce the residual velocities, the viscosity of LVZs is constrained as ~10-10 Pa·s. Our study also suggests that LVZs are probably partially molten, which explains the rheology, seismological, and magnetotelluric data.