Rotor mass unbalance and sensor runout are the main disturbances of harmonic current in magnetically suspended rotor system. Accurate and quick speed detection is the premise of harmonic current suppression. In order to suppress harmonic current in high-speed magnetically suspended motor without the speed sensor， a parallel double input second-order generalized integrator frequency-locked loop （SOGI-FLL） method was proposed. Firstly， the rotor dynamics model of the system was established， and mechanism generating harmonic current was analyzed. Afterwards， the double input SOGI-FLL method was introduced to adaptively estimate the speed， enhancing both the accuracy of speed estimation and dynamic performance. On this basis， the double input SOGI modules were connected in parallel and integrated into the original control system to suppress harmonic current. In order to ensure the stability of the system across a wide speed range， a phase compensation was designed based on the closed-loop characteristic equation and the phase frequency characteristics of the system. To verify the effectiveness of the proposed method， simulation analysis was carried out and a magnetically suspended motor platform was used for experimental verification. Experimental results indicate that the proposed method can accurately estimate the speed， with the tracking error kept within ±0.8 Hz. The first， third and fifth harmonic current components are reduced by 86.20%， 86.16% and 83.86% respectively， proving that the proposed method can suppress harmonic current accurately and effectively.