The South China Sea is rich in mineral resources, and the prospect of developing seabed mineral resources in the South China Sea is bright. However, the South China Sea is also famous for the active internal solitary waves, the researchers detected an internal solitary waves with an amplitude of 240 m and a peak velocity of 2.55 m/s in this area, which may severely impact the deep sea mining system. In this paper, we first simplify the vector finite element method's calculation process. Then the improved vector form intrinsic finite element method is used to simulate the installation process and normal working state of the deep sea mining systems under the action of internal solitary waves. The influence of the internal solitary waves on the deep sea mining systems in the installed state is limited, and its displacement and internal force changes are controllable. Still, the internal solitary waves may cause extensive movement or 180° bends in deep sea mining systems during installation. Necessary measures must be taken during installing deep sea mining systems to reduce the effects of internal solitary waves.