Large-capacity flywheel energy storage systems are mostly used in peak frequency regulation and energy allocation of power systems, which require frequent charging and discharging in actual working scenarios, resulting in the rotor system being under high-speed working conditions for a long time, and therefore require extremely high dynamic stability of the rotor system. The bearing system, as a support component of the flywheel, has bearing characteristics that directly affect the reliable operation of the entire rotor system. In this paper, the dynamic characteristics of the flywheel rotor supported by superconducting bearings are investigated, including the analysis of the vibration pattern and the intrinsic frequency of the rotor, and the influence of the parameters of the superconducting bearings on the dynamic characteristics. Through experimental verification and data analysis, the effectiveness and feasibility of the optimised design scheme supported by superconducting bearings are demonstrated. This study provides important theoretical support for the application of superconducting bearings in high-capacity flywheel systems, which is of great engineering significance for improving the stability and reliability of flywheel systems, and also provides a reference for the subsequent design of superconducting-electromagnetic hybrid bearings.