The application of Cu-filled through-silicon via (TSV) in 3-D integrated circuit packaging faces several fabrication and reliability issues. In this study, we introduced a Cu-Ni alloy for TSV filling with a high filling speed and a reduced TSV protrusion. In particular, the characteristics of Cu-Ni via protrusions at various annealing temperatures (³200450°C) were investigated with experimental and numerical analysis and compared with Cu-filled vias. High speed Cu-Ni alloy filling into the vias was achieved without any defects by an electroplating process that used a periodic pulse reverse current waveform. The Cu-Ni alloy TSV showed lower via protrusion than the Cu TSV. The simulated protrusion heights of the Cu-Ni vias were in good agreement with the experimental results. The simulation results also indicated that the Cu-Ni TSVs has smaller protrusions than the Cu TSVs. As the annealing temperature was varied from 200 to 450°C, the protrusions increased gradually and became significant at an annealing temperature of 350°C. When the temperature was increased further, the protrusions became larger due to severe creep deformation. The von Mises stress also increased with increasing annealing temperature, and increased substantially at a temperature of 300°C due to the creep effect. In summary, the Cu-Ni alloy TSVs showed smaller protrusions relative to the Cu TSVs. The stress level of the Cu-Ni via was lower than that of the Cu via. These results indicate that the Cu-Ni alloy TSV had advantages in terms of high speed filling and smaller protrusions, demonstrating its promise as an alternative to current Cu TSV technologies.