Artificial reefs (ARs) have been widely used to restore the seabed habitat and protect biodiversity. They can effectively increase the dissolved oxygen content in the bottom water layer by their disturbing effect of upwelling and downwelling. The bottom water is prone to hypoxia in summer due to the extreme weather of the global climate and excessive biomass in some marine ranching in northern China. Therefore, how to effectively use the upwelling effect of artificial reefs to alleviate this problem is a necessary subject of research. Generally, ARs are arranged by different intervals in a unit form on the seafloor, and the flow field effect is different from that of the individual reefs. However, few studies have been focused on the effect of layout mode on the flow field of a unit reef (UR). In this paper, we selected the interval between reefs (IR) and the angle of inflow (AI) as the influencing factors to study the flow field effect of UR. The upwelling and wake regions of 64 URs were presented by the efficiency and disturbance indices related to the flow characteristics and proposed an optimal layout mode having the best performance of the upwelling effect. The results showed that the interactions among the AI, the transverse, and longitudinal IRs were significant, and the AI has a significant influence on the flow field. These indices were effective and contribute to the layout optimization of UR. The AI close to 45° has a significant influence on the flow field effect of UR.