<p>Dynamic stability of fractional hydropower generation systems has important significance for the safe operation of hydropower stations. Due to difficulties in the establishment of nonlinear coupling models, the research in this regard is still at the stage of theoretic exploration. This paper focuses on investigating the fractional stability of a hydraulic-mechanical–electrical coupling hydropower generation system in the load rejection transient process. The model of hydropower generation system is established based on the internal characteristic method of the hydro-turbine governing system and the force balance characteristics of the shaft system. The fourth-order Runge–Kutta method is used to solve this complex model with high dimensions. The fractional hydraulic response and vibration response are simulated to evaluate the operation state of the hydropower generation system in the large fluctuation transient process. The rationality analysis of the fractional order is also investigated under 70, 50, and 20% load rejection scenarios. The implemented model contributes to the development of dynamic stability of fractional hydropower generation systems, and the obtained results help reduce the shaft vibrations and operational risks of the system.</p>