Ship floating raft isolation system is an important technology approach which is used to improve the acoustic stealth performance of warships. The influence of raft frame and infrastructure flexibility and the nonlinear isolation is taken into account on the dynamic equations. In the linear condition, the CMD(Calculation of Multi-body Dynamics) software is used to confirm the reasonable of modeling method, and the transmission of vibration energy is researched by the power flow. In the nonlinear condition, method of multiple scales is used to research the dynamic response under the non-resonant state and the numerical solution is used to analyze the differential equation system. The result indicates that the dynamic character of rigid and the flexible raft frame are different in the nonlinear condition. The resonance response could be caused by the harmonic component in the non-resonant frequency.