Three-dimensional water flow field of rectangular artificial reef under various cut-opening ratios was numerically simulated by using CFD technique. Through analyzing the simulated results,the paper revealed the change law of flow field effect to cut-opening ratio that: ① the ratio of the maximum and average velocity of upwelling current to the inflow velocity,the ratio of maximum upwelling height to reef height decrease with the increase of cut-opening ratio; ②the size of the wake vortex region is reduced with the increase of the cut-opening ration, a large wake vortex region with very small flow velocity is formed when the cut-opening ratioes are 0.1 and 0.2, whereas no obvious wake vortex region are perceived when the cut-opening ratio is equal to 0.5 and 0.6. Moreover, the simulation results reveal that the parameters for upwelling current and the map of distribution for velocity field are hardly affected by the magnitude of inflow velocity.