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Capacity proportion frequency allocation compensation parallel control strategy based on the multiple synchronous rotating reference coordinates control is proposed to overcome difficulties in the field of high power application. The zero steady-state error compensation is implemented and the overall stability of the system may be improved by the multiple synchronous rotating reference coordinates control which is carried out as the control strategy of an APF in the parallel system. Therefore, according to the different capacity and the proper optimization, the parallel control strategy achieves the zero steady state error compensation that the APF with large capacity compensates more harmonic current and the one with small capacity compensates less harmonic current, which significantly improves the compensation accuracy and flexibility in the field of high power application. The compensation method based on the capacity-limitation is implemented in order to improve the stability and security. The superiority of the control architecture proposed is verified completely by theoretic analysis, simulation and experimental results.