The invention discloses a control method of comprehensive compensation systems of negative sequence and harmonics in high-speed electric railways. In the control method, current of two feeding sections is subject to comprehensive detection of negative sequence and harmonics so as to generate comprehensive compensation current reference values. Active current of RPC to be transferred is adjusted by calculating a coefficient k of active current of modified first harmonics according to negative sequence compensation indexes. Corresponding control strategies are taken according to service conditions of up electric locomotives and down electric locomotives in high-speed railways: controlling current of RPC converters connected to one feeding section side with running electric locomotives; and controlling DC voltage of RPC converters connected to the other feeding section side without running electric locomotives. A Hysteresis comparison control method is employed for current loops to causeoutput current of converters to track reference compensation current, thus achieving the purpose of negative sequence and harmonic compensation; and DC voltage control is voltage feedback control with inner current loops to quickly stabilize DC voltage. The control method has the advantages of strong reliability, fast control response speed and easy implementation.