This paper proposes a novel 1D-3D approach for the stability characteristics of the hydropower generation system (HGS) in transition processes. First, a 1D-3D coupling model was established for the HGS in the load-reduction process. Second, a sensitivity analysis of the HGS’s parameters to the rotation speed and discharge was conducted. Third, the pressure pulsation characteristics of the HGS with three typical guide vane openings were analyzed during the load-reduction process. The results show that with the closure of the guide vane, the discharge gradually decreases and it is sensitive to the change in hydraulic parameters. The rotation speed fluctuates at the early stage of the transition process and is easily affected by mechanical parameters. In addition, the pressure pulsation inside the Francis turbine is more intense under small openings than large openings, and the primary frequency of pressure pulsation under three opening degrees is the blade frequency. The 1D-3D coupling model successfully integrates the advantages of traditional methods and provides a reference for predicting system stability and exploring the stability mechanism.