Through computational fluid dynamics(CFD) technology, under the unsteady flow, the artificial fish reef three-dimensional fluid fields in six inflow velocities and three kinds of spacing for reef layout were simulated. The artificial fish reef were composed by cube type, trapezoid platform, triangular prism porous hollow monomer fish reefs and combined fish reefs with 20% of penetration rate. The simulated results showed that, the water flow was elevated and formed upwelling current when encountering the upstream which faced to the reef. Under the identical simulated condition, the formed scales and strengths of upwelling and wake the vortex region reached the maximum when the porous hollow artificial reefs of the same type were placed at the 90 degree, while was the second large when the reefs were placed at the 30 degree; the flow field effect generated by cube type fish reefs in case of monomer fish reef was optimal. The analysis of difference in flow fields of combination of nine reefs under different kinds of spacing of reef suggested that, the scale and strength of upwelling increased at first then decreased with the increasing spacing, the reef combination at one time of reef spacing can produce better flow field regulating effect, and binary vortices occurred on the reverse sides of the first group of reefs of cube type and triangular prism reef combinations. Only one vortex occurred in trapezoid platform reef combination. Under identical working condition, cube type and triangular prism reef combinations can give better effects to the fish collection and bait effects as well as the environmental remediation function of the reefs.