Performance of adaptive active vibration control algorithm may degrade if there exists frequency error between the reference signal and primary vibration with multi-line spectra due to the limited situation in the application of active vibration control of water pump. To tackle this problem, an active vibration control algorithm is proposed based on the adaptive feedback FXLMS (filtered-X least mean square) algorithm with adaptive self-generating reference signal. The phase of the reference signal was updated based on geometry relation, besides the frequency of reference signal was estimated by related coefficient based on least mean square method. Simulation and experiment was conducted to validate the effectiveness of the proposed method. Simulation results validates that the algorithm could achieve effective performance by adaptively regulating the frequency of reference signal with the existence of frequency error between the reference signal and primary signal. Experiment of active vibration control of water pump confirms the effective performance of the proposed algorithm.