The slip rates on the Xianshuihe-Xiaojiang fault system (XXFS) are crucial for understanding the strain partitioning and evaluating its seismic risk. Here, we establish a 3D viscoelastic FEM model incorporating the faults as contact discontinuities to gain a numerical image of the XXFS's continuous slip rate. The viscosity of Southeastern Tibet and the locking depth of the XXFS were investigated and constrained by interseismic GPS observations. We estimated that the viscosities of the lower crust and the mantle lithosphere of southeastern Tibet were 1 × 10¹⁸ and 5 × 10¹⁹ Pa s, respectively. The interaction between the Daliangshan fault and the Anninghe-Zemuhe fault governs slip partitioning around the middle part of the XXFS. The XXFS’ overall mechanical efficiency is improved by the initiation and development of the Daliangshan fault. The interseismic strain buildup rate appears to be spatially heterogeneous, depending on the changes in slip rate along the strike of the XXFS. The accumulated strain energy in the Shimian-Miannning and Mianning-Xichang seismic gaps has enhanced the seismic hazard, which should be closely monitored.