For fear of the excessive noise of power capacitors installed in High Voltage Direct Current (HVDC) converter station, the noise characteristics of the power capacitors are necessary to test before delivery. The purpose of the harmonic current injection system is to simulate the actual service condition of power capacitor. To ensure the accuracy of the injected harmonic current, the frequency-domain harmonic current detection and control method is proposed. Based on Fast Fourier Transform (FFT) Algorithm, the amplitude and initial phase spectrum can be tracked timely and exactly. Then the proportional integral (PI) regulator can be used in frequency-domain to track error converging to zero for respective frequency component. The effectiveness of the current control algorithm of harmonic current injection system proposed in this paper is validated by the simulation and experimental results.