We present in this paper a control method of a novel hybrid parallel active power filter (HPAPF) used for harmonic currents elimination and reactive power compensation in the power system for three-phase variable frequency drives (VFDs). The HPAPF configuration is built from two filter components including harmonics tuned passive filter and active power electronics filter. The active power electronics filter of the proposed HPAPF system is controlled by a novel control algorithm that makes use of Fourier analysis to facilitate accurate selective harmonics targeting allowing the cooperation between passive and active components. In the proposed topology, a coupling of the passive filter component and the active filter allows significant reduction in current rating of the active filter component. This rating reduction scheme implies a great economic advantage of the proposed HPAPF compared to the methods which are based only on traditional pure active power electronics filters. The hardware design and the control algorithm of the proposed HPAPF are verified by MATLAB/Simulink software.