The centrifugal compressor is an essential part of the auxiliary power unit (APU) for airplanes and helicopters. As aircrafts are sometimes required to operate at high altitudes, the aerodynamic condition of the gas turbine and APU lies at low Reynolds numbers. This study presents numerical simulations to investigate the effects of low Reynolds numbers on the flow and performance of a centrifugal compressor, including the impeller, diffuser and volute. For the reference Reynolds number (8.4©10 5), the numerical results agreed well with the experimental measurement in total pressure ratio. It was found that the performance of the overall compressor decreases slowly as the Reynolds number decreases, but drops significantly below the threshold of 200,000. The flow inside the impeller didn't separate in spite of thick boundary layers, even at the lowest Reynolds number (8.4©10 4). In this study, it was found that the diffuser is the most susceptible part for separation caused by low Reynolds numbers. The large separation in the diffuser vanes degrades the flow, and decreases the efficiency of the diffuser and volute successively.