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In order to improve the compensating effectiveness of the SAPF, the control strategy has become the research emphases recently. In the paper, firstly present the compensating principle of the three-phase series active power filter. Through analyzing the system, we get the differential equations of the SAPF and set up the transfer function and the block diagram of the exiting open loop control strategy for VSIs. Then, discuss the basic principle of biological immune system. For improving the controlling result of the SAPF, we propose a nonlinear selftuning immune feedback controller. The new nonlinear immune controller is designed by combining the immune feedback mechanism with the conventional PID control. Finally, simulate the close loop SAPF system with the new immune feedback control strategy. Computer simulation results show that the proposed selftuning immune feedback control strategy in SAPF is effective in compensating the voltage disturbance and in tracking a normal sinusoidal reference signal.