Abstract: Shipboard high-power pulse load operation will produce interharmonic current surges and power shocks, resulting in generator bearing vibration, wear and even mechanical failure. In order to solve the problem of unclear quantitative relationship between interharmonic power fluctuation and pulse parameters and the difficulty of interharmonic power compensation under different pulse parameters, this paper proposes a fast tracking adaptive compensation method for interharmonic power fluctuation of shipboard pulse loads, which can quickly respond to pulse load shocks according to the quantitative relationship of interharmonic power and achieve the compensation of interharmonic power fluctuation. The quantitative relationship between the amplitude of interharmonic power fluctuation and the pulse load period, power and duty cycle is established, and its amplitude-frequency characteristic function is obtained. A fast tracking compensation method for hybrid energy storage is proposed, in which the fluctuation spectrum range is obtained according to the amplitude-frequency characteristic function, and the filtering parameters are determined in combination with the power spectrum analysis. The control signal is output after phase delay processing. RT-LAB is used to build a medium-voltage DC naval microgrid model containing pulse loads. The results verify the rationality of the quantitative interharmonic power relationship, showing that the method can realize the optimal coordination of hybrid energy storage, adaptively compensate interharmonic power fluctuations, and enhance the reliability of generator operation.