The high-speed rotor of the flywheel will stimulate micro-amplitude multi-frequency vibrations during operation, which will adversely affect the high-precision attitude stabilization control of the spacecraft, and thus pose a hidden danger to product assurance. This article is based on the problem of microvibration in magnetic suspension flywheels, and establishes a flexible support dynamics model with an algorithm for suppressing micro-vibration. Through simulation analysis, its inherent characteristics are analyzed. The flexible support simulates the magnetic suspension flywheel mounting bracket, and the micro-vibration characteristics of the magnetic suspension flywheel active vibration isolation system supported by three different stiffness T-shaped cantilever flexible supports are compared to analyze the impact of flexible support on the performance of the magnetic suspension flywheel active vibration isolation system. The results show that the active vibration isolation of the magnetic suspension flywheel does not change the natural frequency of the system structure. The disturbance force formed by the coupling of natural frequency and harmonic vibration frequency becomes the main disturbance component, and the power frequency disturbance force is no longer the main disturbance component. The current active vibration isolation algorithm helps to suppress system micro-vibrations on supports with high stiffness.