Due to the limitation of the machining accuracy, there exist mass imbalance and sensor runout in magnetically suspended rotor system, which will result in harmonic current in the rotor system. Harmonic current can not only increase the power consumption but also induce harmonic vibration which will be transmitted to spacecraft by magnetic bearings and affect the attitude stability of spacecraft. In order to analyze and reduce harmonic current, the model of magnetically suspended rotor system is built and analyzed. Variable-step-size FBLMS algorithm is proposed in this paper to suppress harmonic current simultaneously. According to the proposed algorithm, step size variation depending on harmonic current and individual step size is figured out for each weight vector so that each frequency component in the block can be adjusted. As a result, convergence performances are further improved by adjusting the weight vectors adaptively. The validity of the proposed method is testified by simulation. Simulation results show that variable-step-size FBLMS algorithm can reduce the harmonic current further and increase the convergence rate.