This paper proposes a new voltage reference generation method for Four-Switch Inverters(FSI) with compensation of the neutral DC-link voltage variation. Since FSIs have the split DC-link causing the inherent problem of voltage fluctuations in the upper and lower capacitors, it is required to take account the voltage difference between the top and bottom capacitors. In this paper, to reduce the effect by the voltage variation, reference voltages are modified by adding compensation voltages proportional to the voltage difference between upper and lower capacitors. Simulation results showing control performance of induction and permanent magnet motors demonstrate the validity of the proposed method.