Different shapes,sizes,and the combinations of the artificial reefs can affect the upwelling and the back eddy flow.Considering the artificial reef in the sea can cause certain alteration to the flow around it,by using the Large Eddy Simulation (LES), a method of Computational Fluid Dynamics,this paper tries to design different structures of a cubic reef through x /y /z three directions,then we can study the connection between the structures and permeability.The result showed that the ranges of the upwelling and back eddy flows decreased as the increase of input and back-output permeability strongly;but the effect from the permeability of internal structure and the permeability of direction y and z are not very clear.So the InputPermeability is the main effect factor of the range of the back eddy flows.The volume of the back eddy flows around a cubic artificial reef decreases as the increase of the Permeability T_m,the equation is V_x=-1241.8T_m + 1206.According to this study,we can use the relation between the permeability and the change of the flows;so that we can simplify the reef with complex structure in the 3D numerical simulation as well as the improvement of computed speed;Based on this research,we can apply the small range simulation to the large area in order to evaluate the ecological effect of artificial reef.