A method of fatigue damage analysis for sandwich panels on ship is studied in this paper. When ship is navigating on the sea, the waves that ship encounters can be regarded as a stochastic process. And responses of ship movement can also be regarded as a series of stochastic spectrums. By using of finite element method, loads spectrums of inner ship structures in different sea conditions can be obtained. Then short term or long term distribution of stress range can be determined. Residual stiffness modal is used to describe the damage of sandwich panels under fatigue loads. And fatigue damage variable D is defined based on stiffness degration. An integral equation to calculate fatigue damage under loads spectrum is constructed to describe the damage of ship sandwich structure in long term and short term stress spectrum distributions.