A unified control method of comprehensive compensation system based on CS- APF and SVC is introduced in this paper. SVC is composed of thyristor controlled reactor (TCR) and fixed capacitor (FC). For the CS- APF control, a feedforward control for harmonic compensation of SVC and load is applied. The CS- APF is enabled to optimize the var compensation performance of SVC. Finally, the simulation results show that the system can effectively compensate reactive power and eliminate harmonic currents.