Polymer liner has been used in through-silicon-vias (TSVs) for smaller parasitic capacitance and better thermo-mechanical performance. For the application in heterogeneous integrated systems, it is critical to study the thermal reliability of such TSVs in both theoretical modeling and experimental characterization. Among the numerous reliability challenges, the Cu protrusion phenomenon of TSVs is one of the most severe issues, which can lead to cracks and delamination in integrated systems. In this article, the annealing-induced Cu protrusion of polyimide (PI) liner TSVs is studied by experiments and simulations. PI-TSVs are fabricated and the Cu protrusion at various annealing conditions is characterized. Finite element analysis (FEA) is carefully carried out taking into account the diffusion creep rate model, and the deviations between FEA and experiment results of protrusion heights are less than 3%. Besides, the deformation procedure and the creep behavior of Cu pillars during annealing are analyzed. Based on the proposed FEA model, comprehensive parametric analyses are conducted to study the effects of different annealing conditions on the Cu protrusion heights, which are helpful to understand and improve the thermal reliability of PI-TSVs.