The invention provides a flywheel rigidity parameter extraction method based on a micro-vibration waterfall plot. The method comprises the steps of: (1) building a radial kinetic model and a radial micro-vibration transmission model of a flywheel rotor; (2) testing micro-vibration during speed rise of the flywheel and generating a waterfall plot; (3) obtaining local peak value coordinates on the micro-vibration waterfall plot of the flywheel; (4) based on classification and robust regression of the coordinate data, obtaining function expressions of a mode and vortex motion curve in a full rotating speed range through fitting and performing transposition multiplying on the four expressions to obtain a structure feature polynomial; (5) obtaining an optimized target function; (6) solving thetarget function through an optimal method to obtain rigidity parameters in the radial kinetic model and the vibration transmission model of the flywheel. The method can be applied to optimal configuration of rotor structural rigidity, vortex motion and modes during flywheel design and can serve as proof for judging the consistence and the qualification of product structures in a mass production process of flywheels.