With the increase of high-reliability requirements, the multiphase machine draws considerable attention from the field of transportation electrification. However, the presence of third-order harmonic subspaces in five-phase machines poses greater challenges for high-speed applications, particularly due to the low sampling-to-fundamental(S2F) frequency ratios observed in higher-order subspaces. In this case, the electrical speed in third-order harmonic subspace is three times of that in fundamental subspace. The closed-loop control system performance deteriorates gradually or even becomes unstable due to cross-coupling in dq axis. Therefore, a Smith predictor-based decoupling control is proposed to eliminate the cross-coupling at low S2F frequency ratios. Additionally, the proposed method offers a solution to ensure the control stability of high-speed five-phase motors.