This paper deals tilth an efficient algorithm in spectral fatigue analysis of ship structures. The concept of stress influence coefficients is suggested in order to obtain stress transfer functions efficiently which are the structural responses for unit load components. Strip method is applied to obtain the motion response and pressure distributions exerted on the hull. Since a number of the structural analysis should be performed for the various wave frequencies and heading angles in the spectral analysis, the algorithm developed in this study improves the efficiency of the analysis. Finally, the calculation example with application to this concept is shown in this paper.