In the isolated island microgrid system, a second-order filter is introduced to reduce the impact of measurement noise. However, the introduction of the second-order filter usually changes the optimal parameters of the original PID controller, which leads to the decline of the performance index of the control system. To solve this problem, this paper proposes an integrated parameter setting method. In this method, the hybrid particle swarm optimization algorithm is used to optimize the high score of system performance index in Topsis comprehensive evaluation method under different parameters, and the parameters of PID controller and second-order filter are integrated to ensure that the introduction of filter will not cause great changes to system performance index, so as to improve the controller performance. The feasibility and effectiveness of the proposed method are verified by the simulation experiment of isolated island microgrid system.