The unbalanced magnetic pull (UMP) of hydro turbine generating sets (HTGS) is one of the main reason induced vibration of the HTGS and the power plant. To study the effects of UMP on the shaft vibration characteristics of HTGS, this article constructs whole HTGS system which include hydraulic turbine and its hydraulic system, generator, transient model of the HTGS shafting, excitation and governing system, to simulate the actual operation of HTGS. The shafting vibration is simulated under different characteristics of UMP, simulation shows that the frequency resonance zone of the UMP has large influence on the shafting vibration. And then, the improved Prony algorithm is applied to extract the shafting oscillation characteristics of HTGS, and is effective. It provides a good method to research the effect of frequency and amplitude changes of UMP on the shafting vibration.