With the fluid simulation software (Ansys Fluent) and turbulence module (large eddy simulation, LES), we have simulated the flow field effects of four different types double layer cross-airfoil artificial reef. To quantify the flow field parameters, including the volume of upwelling and wake vortex, and the transport flux by upward waters, we adopt the method of concrete volume ratio to obtain the optimal structure of artificial reef, in order to provide a scientific basis for the design and selection of artificial reef. The simulation results show that the double layer cross-airfoil artificial reef with roof has faint effects on flow field, the relative volume of upwelling and wake vortex become smaller. While the artificial reef with side plate has obvious effects on flow field, the relative volume of upwelling and wake vortex increase gradually. Similarly, the flow effects of upwelling and wake vortex of D-type reef with full-side plate are most strongest, and the relative volume of the upwelling can reach 13.50-25.48 times of the B-type reef without side plates, the relative volume of the wake vortex can reach 1.40-1.61 times; the maximum transport flux value of upward waters appears at 1 times height of the reef, and about half of the maximum value appears at 2 times height of the reef. The result also shows that there is no evident difference in the flow field effect of D-type reef when changing the upstream angle, which indicates that this type of reef has a good adaptability to the flow direction in the natural sea area.