The three-dimensional structure of the summertime circulation of the Yellow Sea (hereafter YS) is studied by using a prognostic wave-tide-circulation coupled model based on the Princeton Ocean Model (POM) and a surface wave model. The simulated tidal harmonic constants and temperature structure agree with the observations well. The patterns of the simulated salinity generally agree also with the observations. The simulated results show that the horizontal circulation has a three-layer structure: in the surface layer (0--4 m), the prevailing current direction is northeastward; in the upper layer (4--40 m) it is dominated by a basin scale anticlockwise (cyclonic) gyre; in the bottom layer (below 40 m) the water diverges from the center area and there exists a weak southward current along the YS trough. The stream function of the YS shows that the net circulation of the YS is an anticlockwise (cyclonic) one, and the net transport is about 0.1 Sv. Diagnostic analysis of the momentum balance and sensitivity show that the cyclonic circulation in the upper layers is mainly a quasi-geostrophic flow along tidal-induced temperature front, and it is also strengthened by the tide residual currents. The tidal residual current and the compensation for northward surface layer wind transport contribute to the formation of southward flow in the bottom layer. The vertical circulations vary along different sections. A circulation cell is found in the frontal area near the Korean coast, and an upwelling is found along the slope.