With the connection of distributed new energy to a charging station, the random characteristics of source and load cause fluctuations in the fundamental frequency of the power grid, aggravating the risk of harmonic current off-limit in the station. Therefore, a frequency adaptive active power filter harmonic detection and tracking strategy is proposed. First, a hybrid filter structure combining an improved generalized integrator and delay signal cancellation is designed to enhance the filtering performance and dynamic response capability of the original generalized integrator, and to eliminate the influence of DC bias and unbalanced components. Secondly, by introducing an improved phase locked loop with feedforward compensation, the error caused by frequency fluctuations is eliminated, achieving frequency adaptive harmonic detection. Finally, based on the harmonic tracking error caused by frequency fluctuations, a fast repetitive control combined with an infinite impulse response filter is proposed. This can be dynamically adjusted according to the detection frequency. The simulation and experimental results show that the proposed control strategy can stably detect the grid frequency on the charging load side, and has better harmonic compensation ability in conditions of frequency fluctuation. It can compensate for harmonic currents in 32 ms and reduce the current total harmonic distortion to less than 5% after treatment, and it is universal for charging stations in different operating conditions.