The tsunami propagation and coastal run-ups generated by the 2006 Pingtung earthquake doublet is studied numerically. The numerical model – COMCOT, which adopts a modified Leap-Frog finite difference scheme solving nonlinear Shallow Water Equations (NSWE), is employed. The assessment of the tsunami amplitude and extended effects is discussed in this paper using a set of nested bathymetric grids with a decreasing cell size focused on southern Taiwan. The three nested grids cover from the large far-field South-China Sea to the small near-shore regions. Several possible fault plane mechanisms are examined. Based on the arrival time at different tidal gauges, the suggested seafloor displacement is presented. Adopting the relocated seafloor movement with the fault parameters issued by Global CMT, the model results are favorably compared with the field tidal gauge wave form data. The result shows that the tsunami amplitude is about 35 cm and about 20-min period with the first depression at SyunGuaggZuei. Aworse case scenario, Mw = 8.0, is studied. The maximum water levels can reach 4 m for Mw = 8.0 along the shoreline at HouBiHu.We also observe that owning to the source geometries and to the trapping of the tsunami energy by edge wave effect, the south-east coast of Taiwan coast is one of the most dangerous zones for the South China Sea earthquakes.