Abstract: Operational modal analysis is a procedure which allows extracting modal parameters from a structure in operational condition only based on response data under ambient excitations. The input to the structure is assume d to he a stationary white noise. In practice however, the excitations on a ship during voyage can not be assimilated to white noise input, harmonic forces produced by the main engine and propeller are also presented, so the excitations of an operational ship can be assumed to be white noise including harmonic excitations. The application feasibility of operational modal analysis on a ship structure was discussed. And the auto-cross spectrum density method was proposed and verified by a simply supported beam experiment. Then the vibration data of the mast during trial was analyzed and discussed.