A novel large reinforced HDPE cage system applied for the deep-sea aquaculture is proposed in this paper. This new structure is targeted at two main challenges facing by the deep-sea aquaculture. First, the deep-sea operation condition is much more complicated than in near shore area; second, the dynamic response and structure requirement of large-scale cages, which can be up to 80–100m in diameter and are significantly different to that of small HDPE cages. This study tackled with these two challenges by using the reinforced HDPE material and nested floating frame structure. In order to examine the integrity, safety and structure performance of this presented structure, the dynamic response of the structure subject to various working conditions are numerically simulated and analyzed in this paper. Simulation results of the new structure are compared to that of the traditional cage regarding the cage dynamic displacement, maximum strain/stress and net declination angle. The deformation results demonstrated that the maximum strain and stress on the cage collar of the new structure is much smaller than that of traditional design, and thus the new design can greatly reduce the local deformation of the cage collar and the declination angle to ensure the structure safety in severe sea conditions. The internal nested float frames can also be arranged with nets to make better use of the breeding space.