The shafting vibration for the Hydraulic-Turbine Generator Unit (HGU) inevitably affects the safe and stable operation of the Units. Excessive shafting vibration could cause fatigue damage of materials, which eventually leads to malfunction of HGU and even results in damage accidents in serious cases. Generally speaking, the vibration is mainly generated from the high-speed rotation of the shafting, and mechanical, hydraulic, and electrical factors as the vibration exciting sources may be coupled all to cause a vibration of the HGU, so it is necessary to take the whole shafting as a specific object of study. In recent years, many scholars have conducted much research on them and their results are focused more on how to control the influence of external excitation sources of vibration, but still lack consideration of the shafting’s internal mechanism of vibration. In this paper, a predictive analysis method is proposed to reveal the internal mechanism of vibration. Starting from the analysis of natural vibration characteristics of the shafting, this study establishes the finite element calculation model of the shafting of the HGU based on the finite element analysis method. By selecting appropriate research methods and calculation procedures, the modal analysis of the dynamic characteristics of the shafting structure is carried out. Finally, the first ten-order natural vibration characteristics and critical rotational speed of the shafting structure are successfully calculated, and the results conform to the basic laws of shafting vibration. In addition, by comparing the relationship between rotational frequency such as the rated speed, runaway speed, and critical speed of the shafting, the possibility of resonance of the HGU is analyzed and predicted, and then some suggestions for optimization design such as increasing the shafting’s stiffness and balancing its mass distribution are proposed. Therefore, this study provides a basis for guiding the structural design and optimization of the shaft system in engineering, and avoids the resonance caused by the excitation source such as rotational frequency, thereby ensuring the safe and stable operation of the HGU.