Opening holes, especially circular hole, in artificial reef block is a conventional choice in design of artificial reef. However, there is less scientific study about how to select the hole diameter. In this article the performance of the rotary-shaped artificial reefs with different size of circle holes was investigated using CFD method and the orthogonal experiment design. The reef having the best performance was identified. The results indicate that the design of interlaced hole diameter can significantly promote the flow field scope, especially the height of upwelling, in comparison with that with the uniform hole diameter. There is no obvious relationship between the cut-opening ratio and flow field effect for the rotary-shaped reef. This work supplies a scientific evidence for how to select the hole diameter for an artificial reef.