<p>The shift of marine aquaculture from nearshore to offshore has become prevalent in the world. The geographical conditions of many countries determine that deep-sea aquaculture needs to be carried out in open waters, which requires higher safety standards for net cages. Floating net cages are the most common type in deep-sea net cages. In numerical modeling of deep-sea cages, the potential flow theory and Morison equation are two common methods. In this work, two complete net cage models based on each theory are established, including the main structure, mooring and net system. The simulation results indicate some deviations in the motion and anchor chain tension calculation between the results of the two models. The choice of the additional quality coefficient impacts the results. Considering the safety requirements of the floating cage design, the potential flow theory is an accurate numerical method, and the Morison equation is a good alternative for tasks that leave a large safety margin, such as mooring design. This study provides some suggestions for the selection of numerical methods for the hydrodynamic performance calculation of deep-sea floating cages in the future.</p>