In order to eliminate the input current harmonics and dc-link voltage ripples of Vienna rectifier under unbalanced input, a novel control strategy applicable to wide variable frequency (360–800 Hz) aircraft electrical system is proposed in this article. To serve this purpose, current references on natural frame are first derived, which contain quadrature signals of grid voltages. Then, a natural-frame-based control strategy is designed, in which the second-order generalized integrator (SOGI) frequency-locked loop (FLL) is employed for variable frequency grids. Compared with traditional dual-frame control strategy, the proposed strategy reduces the algorithm complexity and has better frequency adaptability. The proposed strategy is suitable for all the unbalanced conditions, which is defined by test procedures DO-160G. Simulation and experimental results verify the effectiveness of the proposed control strategy.