An artificial floating reef is an important part of the coastal ecological corridor. The large-scale construction of floating reefs by optimizing mooring methods can effectively improve the ecological effects of coastal projects. The artificial floating reef belongs to coastal engineering, and wave resistance is fundamental to its structural design. In this paper, the method for processing coupling forces and motion, the method for judging the floating reef out of water surface, and the method for correcting velocity and acceleration of water mass points are elaborated in detail by using the finite element method and lumped-mass mooring model. By comparing and analyzing the results of physical experiment and numerical simulation, the correctness of the numerical model is verified. Finally, the diachronic variation of pitching angle of floating reef, the tension of the mooring rope, and the total tension of the fixed points of the fishing net were analyzed by the dynamic response numerical mode with a new type of mooring. The purpose of the current study was to provide a basis for the optimization of structure shape, the matching of floating body, and the counterweight of artificial floating reef.