Aiming at the error problem in estimating the speed of a permanent magnet synchronous motor(PMSM) using a sliding mode observer in a flywheel energy storage system, a super twist sliding mode observer(SMO) is used to replace the traditional sliding mode observer. A new saturation function is designed to replace the sign function. In addition, a constant sliding mode gain may lead to a decrease in observation accuracy during speed switching. An adaptive sliding mode gain is proposed to reduce chattering, The accurate estimation of the comprehensive speed range observer is enhanced, and the stability of the proposed observer is proved. On this basis, a super twist sliding mode speed controller is designed to replace the traditional PI controller to improve the observation performance of the system. The flywheel energy storage system's simulation model is built, and the flywheel energy storage system's constant speed standby and charging conditions are simulated. The simulation results verify the correctness and effectiveness of the improved super twist sliding mode observer in the flywheel motor.