This paper proposes a FPAA-FPGA/DSP-based mixed signal controller that achieves superior performance when compared with conventional digital controllers in power quality compensation. This includes adaptive signal conditioning and programmability on-the-fly, higher flexibility, parallel computation capability, and easy implementation. In practical applications, the power quality compensator may suffer from poor compensation performance, particularly during light loading. The adaptive signal gain and programmable on-the-fly functions of the mixed signal controller are intended to improve the system compensation performance, which cannot be achieved by using conventional digital controllers alone. In this study, an approximate total harmonic distortion (ATHD) is proposed to determine the total harmonic distortion value more quickly, reducing the evaluation time of the power quality compensation system performance. With hysteresis pulse width modulations, when the hysteresis error margin is designed, the ATHD can be determined instantaneously. Finally, representative simulation and experimental results of a three-phase four-wire center-split hybrid active power filter are presented. These verify the validity and effectiveness of the proposed mixed signal controller in improving current quality compensation performance during light load conditions, compared with a conventional digital controller.