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Three phase Phase-Locked-Loop is an important part of active power filter. In order to improve the behaviors of the conventional PLL system (CPLL), a novel control method of variable gain nonlinear PI controller based three phase PLL system (NLPLL) is proposed in this paper. As the proportional gain and integral gain of the nonlinear PI controller can adapt variety of the phase error, the schematic of the proposed is better than conventional PI controller in phase tracking velocity and phase tracking precision. The principle of three phase PLL system is introduced, and the design of the nonlinear PI controller is analyzed in detail. The results of simulation show that the proposed method can improve more effectively performance of the tracking speed and the tracking precision and meets the requests of the performance of high precision and real time for harmonics detection of active power filters.