Abstract: The South China Sea version(SCS-POM) of the U.S. Princeton University Ocean Model(POM) is used to simulate the effects of the bottom topography of the South China Sea(SCS)on currents, sea surface heights and temperatures in this paper. Four numerical experiments are conducted by use of steep(STP), Smooth(SMT), plain(PLT) and mediate(MDT) bottom topography respectively, in the model. With the real coast lines and the January wind stress forcing, the model is time integrated up to 360 days and the results are comparatively analyzed.It is found that important influences of the bottom topography exist on the water mass trans-portation and the temperature, while less importance appears in the effects on the surface and the shallow-layer currents, and on the free sea surface height as well. They are mainly deter-mined by the joint effect of the coast line and the wind stress. Some opinions on how to select the ocean model in an ocean-atmosphere coupled model are put forward in this paper, too.