Abstract: In order to improve the scientificity of artificial reef construction site selection and reef body design, we carried out the physical model tests of the local scour and deposition of two kinds of artificial reefs on silty clay based on experimental flume. Through the topographic survey and theoretical analysis, we investigated the local scour and deposition of five groups of different reef structures (two kinds) artificial fish reefs at different velocity. The results show that when the flow rate of silty clay was less than 0.22 m·s⁻¹, the sediment disturbance and the local scour around the two reefs were small, and the main form of erosion and deposition was the accumulation of floating sand near the reef floor, which increased with the increase of velocity. When the flow velocity was greater than 0.22 m·s⁻¹, the scour pattern was more obvious. The scour pit range and depth around the reef increased with the increase of flow velocity, while the sediment accumulation height around the reef decreased. The scour phenomenon of Reef A with complex supporting structure was significant and complex. The maximum scour pit depth was −15 mm at the bottom of the middle of the reef, and the long tail sediment accumulation occured at a height of 1 times of the reef behind the reef, which reached the maximum value of 5 mm at the flow rate of 0.27 m·s⁻¹. However, the scour phenomenon of Reef B was not significant. Only a small amount of accumulation and scour pit appeared near the bottom plate, and its settlement was caused by the relatively large floor opening. Therefore, in the future research, the supporting structure and floor of the reef should be optimized and the model test and numerical simulation should be carried out in combination with the sediment and hydrological characteristics of the selected sea area for site construction, so as to avoid the phenomena of settlement, burial and bed surface hollowing of the reef.