An oil-free turbo-compressor supported by compliant foil bearings which remove oil-contamination by elimination of a conventional ball bearing and oil lubrication systems is presented. Turbo-compressor makes two individual air compressions with two impellers at a operating speed of 39,000 rpm. In this study, the rotordynamic effects caused by aerodynamic instability were investigated with variable mass flow rates. Correlations between frequencies of pressure fluctuation in two diffusers and those of excitation forces on rotor were clearly observed in an aerodynamic unsteady region. Thus, these results show that it is beneficial to design high-speed rotating turbomachinery by considering coupling effect between aerodynamic instability and rotordynamic force.