The operating parameters of hydroelectric generating system vary constantly in the course of transition, meanwhile, the coupled correlations among hydraulic, mechanical, electrical and structural subsystems are convoluted, which makes the vibration of shafting system prominent, as well as affects the safe and stable operation for hydropower station. In this paper, a coupled hydraulic-mechanical-electrical-structural model for hydroelectric generating system is proposed, while the start-up transient process is incorporated into the investigation system, and the dynamic response from shafting system at different stages attached to start-up process is scrutinized numerically, making allowance for the effect of unbalanced magnetic pull with static and dynamic eccentricity. The kinetic property of structure over the start-up process is illuminated, by means of the comparison with motion trait for system under steady-state operating condition. The results indicate that the dynamic feature of rotor and runner is significantly contrasting in different stages affiliated to the start-up scenario, especially for the voltage building-up subdivision. In addition, the response peculiarity from rotor covering the trajectory, vibration amplitude and frequency components, etc., is markedly altered, due to the participation of static, dynamic eccentricity as well as the matching variation on electromagnetic excitation. The trajectory of rotor evolves from a regular circle to a butterfly-shaped curve, and the associated transient displacement intensifies immensely, besides, the 2x frequency component emerges and corresponding dominant role gradually strengthens, accompanied by a developmental amplitude of 1x frequency in spectrum diagram. Relevant research results can provide profitable reference for the analysis of dynamic characteristic on hydropower station through transient conditions.