Hydraulic instability is a complex factor causing the vibration of hydro-turbine generator shafting system (HGSS), and the mechanism is the uneven distribution of flow along the circumference. The common reasons for this phenomenon include the inconsistency of the blade exit flow angle, the relay stroke and the guide vane opening. This paper mainly focuses on the research of the hydraulic instability caused by the inconsistency of the blade exit flow angle. Firstly, based on the Kutta-Joukowski theorem, the hydraulic unbalance force model is firstly presented. Then, considering the chain reaction among the hydraulic, mechanical and electrical instability, a combined nonlinear mathematical model of the HGSS is established. Finally, by using numerical simulation, the dynamic characteristics of the HGSS with the changing of the deviation of the blade exit flow angle, the blade exit diameter and the guide vane opening angle are analyzed. Moreover, it is found that the hydraulic instability determines the overall changing trend of the shafting dynamic behaviors. In addition, some stable ranges of the HGSS are distinguished. But above all, these results can efficiently provide a reference for the design and manufacture of hydro-turbine blades and the operation of hydropower stations.