Artificial floating reefs are an important supplement to bottom reefs in marine habitat construction, which provide a good environment for fish to survive, breed and habituate in the middle and upper layers of water. They can adapt to the silt bottom of the East China Sea. To make full use of the water space and improve the effective space of the floating reef, based on the field tidal current data, an upper- and lower-layered artificial floating reef has been designed in this study. The connection method of the upper and lower reefs has been described in detail and a hydrodynamic numerical model has been established. At the same time, the effects of floating reef structure ratio, wave height and wave steepness on its force and motion are discussed under the action of tidal current and wave current. The result shows that, at a specific flow rate, the change of the proportion of the layered floating reef structure had little effect on the roll of the upper and lower reefs. The maximum roll angle does not exceed 15°, and the tilt angle of the upper and lower reefs is consistent, which ensures the good flow resistance and stability of the floating reef. Under the specific length of the connecting cable and the main mooring, the hydrodynamic characteristics of the layered floating reef are better when the ratio of the sum height of the lower reef and the connecting cable to the height of the upper reef is not greater than one and the extreme proportion structure is not considered. The tension of the stratified floating reef is proportional to the wave height and wave steepness under the action of wave and current. The main mooring rope is the most stressed, and the rolling motion of the upper and lower reefs is consistent. Above all, results can provide a theoretical basis for the optimization design of the artificial floating reef structure.