A numerical investigation on the aerodynamic effects of impeller-diffuser axial misalignment in the low-flow-coefficient centrifugal compressor is conducted through three-dimensional CFD analysis. The results show that the flow, especially near the diffuser inlet, is influenced by the axial misalignment obviously. When the impeller offsets to one side, the pressure at diffuser inlet close to this side will descend, and the vortex in the cavity on the other side will partially enter the diffuser and then result in the back flow. The performances of the stage and its components also change with the impeller-diffuser axial misalignment. There exists an optimum offset making the efficiency maximum at a given operating point. Furthermore, the effect of impeller-diffuser axial misalignment on the axial thrust is pronounced. The axial thrust is nearly increased linearly with the increase of axial misalignment. The aerodynamic effects of impeller-diffuser axial misalignment in the low-flow-coefficient centrifugal compressor behaves more remarkably at the large flow rate. To alleviate the aerodynamic effects of impeller-diffuser misalignment, a rounding in the meridional plane at the diffuser inlet can be applied.