There is a stability problem in traditional generalized integral control. We propose a harmonic compensation method based on improved generalized integral control to enhance the compensation performance of the active power filter. By introducing a first-order differential link into the traditional controller, the poles of the controlled object are cancelled and the order of the system is reduced, so the phase margin of the system is improved. At the same time, a multi-channel improved generalized integral control structure in the synchronous rotating coordinate system is constructed so that the number of improved controllers and the controller parameters to be set are reduced by half, the design complexity is reduced and the problem of filtering frequency cross is effectively avoided. Then the influence characteristics of the controller's key parameters in the discrete domain are analyzed. The evolutionary trend of system stability under different integral coefficients is obtained and system stability check results show that the parameter design is reasonable. Finally, the feasibility and effectiveness of the proposed method are verified by simulation.