Three-dimensional water flow fields past a three-prism artificial reef with three meters long of each side are numerically simulated by using the commercial CFD software (ANSYS FLUENT) under the five different incoming velocities (0.1,0.2,0.4,0.6and 0.8meter per second respectively).The position of the maximum velocity of the upwelling current, the maximum upwelling height, the maximum and average velocities of the upwelling current as well as the size of the wake vortex region are all obtained through analyzing the numerical results of the velocity fields, and the wake vortex structures and pressure distributions are analyzed. Moreover, the flow discrepancies are revealed when the flow passes between a rectangular artificial reef and a three-prism artificial reef.