As the frequency of the ship power system is more likely to fluctuate than that of land power system and the fluctuation range is bigger, the data compatibility scheme of hybrid measurement in the land system based on the invariant frequency can’t be applied to the ship system without correction. To solve this problem, a data compatibility method of PMU/SCADA hybrid data based on the accuracy frequency tracking and the data relevancy analyzing is proposed. The frequency is detected according to the frequency tracking algorithm based on the adaptive notch filter and the PMU data. A data compatibility scheme that can apply to the ship power system is proposed base on the influence of time-synchronization and weight of the hybrid measurement data on the state estimation, of which the correctness and effectiveness is verified by simulations. The proposed method makes that when the frequency of ship system fluctuates, the data of SCADA is corrected and is compatible to the PMU data in time-synchronization and weight.