3-D modeling of through-silicon-via (TSV) with sidewall scallops, combined with an element birth and death technique, is explored in finite-element analysis (FEA) in this paper to evaluate and improve the thermo-mechanical reliability. Compared with the classic FEA, the proposed modeling and simulation method takes into account the process sequence and, hence, can accurately characterize the stress distribution and fluctuation phenomenon of TSVs, which agrees pretty well with X-ray experimental data. In order to solve the stress fluctuation problem, the process-friendly polyimide dielectric liner is employed to replace the SiO2 liner, which smoothens the sidewalls, reduces the average stress values, and eliminates the local stress fluctuation. The average stress on TSVs with a polyimide liner along the silicon-liner interface and copper-barrier interface are both lower than TSVs with an SiO2 liner and the fluctuation magnitude is also dramatically decreased, which demonstrates that the TSV with a polyimide liner has higher reliability and lower risks in interfacial delamination. Furthermore, the keep-out zone size is also decreased by using a polyimide liner, which is beneficial to realize high-density 3-D integration.