Performance evaluation of a hydropower generation system is a critical science and engineering problem, with ubiquitous presence in hydropower plant applications. This study aims at a nonlinear model of the hydropower generation system with multiple units, where a novel modeling methodology for the start-up transient process is presented. Experimental data from an existing hydropower station are considered to validate the established model. The numerical result obtains the effective intervals and possible optimal values of the critical system parameters to diminish the operating risk of hydropower stations. The result also shows the interaction effect of the multiple units and the vibration performance of the system in the start-up process. The implemented application has an interface with the effective evaluation for the safety strategy of the HGS in the actual transient operation, and the obtained results have good precision and are in agreement with theories and engineering applications. © 2019 Elsevier Ltd