Sinking and floating reefs are the main types of artificial reefs, and have been widely used in the development of marine ranching. The floating reef is usually used to trap and protect fishes distributed in the middle and upper water layers. Compared with a sinking reef, the floating reef is less restricted by seabed conditions and demonstrates better performance in the seabed with silt substrate. However, the floating reef can be greatly affected by the dynamic ocean environment, such as waves and current, as its main body is set in the middle and upper water layers. Thus, the structural safety and stability of floating reefs are key points for their design and deployment. This study proposes a newly designed multi-functional cage-net floating reef characterized by its function in both fish protection and culture. Moreover, a numerical model has been established to analyze the effects of wave height and water depth on the structural safety and stability of a floating reef anchored by two modes (single anchor rope and multiple anchor ropes). The results showed that under the same hydrodynamic conditions, in the case of a single anchor rope, the total anchor rope force was almost the sum of the forces for the four anchor ropes; however, the total netting force was less than that in the case of four anchor ropes. Wave height had a great influence on the maximum deflection angle of the floating reef. However, anchoring with four anchor ropes can significantly reduce the maximum deflection angle; the reduction becomes more obvious with increasing wave height, effectively improving the stability of the floating reef. Under conditions of constant wave height, the maximum offset of the floating reef decreased rapidly with increasing deploying water depth. Furthermore, there was minimal difference in the movement of the floating reef between the two anchoring modes when the submergence depth of the main body was twice that of the wave height.