To compensate the negative sequence and harmonic current of the traction power supply system, a comprehensive compensation scheme is proposed. The comprehensive compensation system is composed of railway power controller (RPC), thyristor controlled reactor (TCR) and thyristor switched capacitor (TSC). The working principle of the device is analyzed, and instantaneous current detection method based on the principle of phase demodulation is adopted to extract the active and reactive component in the load current. The reactive current allocation strategy is proposed to provide trigger signal for TSC and TCR. TSC and TCR are used to compensate the shortfall of reactive current for the heavy-loading and light-loading supply arm. Compensation capacity of RPC is greatly reduced, only providing negative sequence current, harmonic current of the traction system, and a small amount of reactive current used to adjust the actual compensating capacity of TSC, achieving the effect of negative sequence compensation and harmonic suppression. Simulation and experimental results show that the device has a strong ability to compensate negative sequence current and a good harmonic suppression ability, suitable for engineering application as a low cost.