The flywheel energy storage system using superconducting magnetic bearings is a device to store electrical energy as rotatioal kinetic energy by motor and to convert it to electrical energy by generator when it is necessary. The rotordynamic analysis should be performed with an adequate analytical model and equations of motion to identify the stable driving condition and the dynamic behavior. The critical speed and the unbalance response of superconducting magnetic bearings-flywheel system are studied in this paper. The analytical results show that the system has one forward whirling mode and two backward whirling models below 500rpm. The maximum displacement 0.75mm is detected at the first forward mode (385rpm)through unbalance response analysis. The analytical results are compared with the experimental result by the spin-down test. The experimental result shows that the maximum displacement is 0.7mm at 370rpm.