Because a pump-turbine mainly undertakes the role of energy conversion and pumped storage in the field of hydropower engineering, the complex transition process and frequent conversion between different working conditions lead to the increase in the stress and strain of core components such as the unit shaft system, and even cause resonance phenomena. Based on ANSYS finite element numerical calculation software, this paper adopts the acoustic fluid–structure coupling method to study the influence of the shaft of the pump-turbine on the dynamic characteristics of the runner. At the same time, the paper analyses the influence of different contact modes between the runner and the shaft on the modal characteristics of the shaft system. The numerical simulation results have shown that the runner is affected by the added mass of the water. The natural frequency reduction rate of each order of wet modal is ranged from 19% to 64%. The main shaft has a greater influence on the simplification of the shaft system calculation method. The type of contact surface between the main shaft and the runner has a smaller influence on the modal characteristics and the natural frequency of the shaft system. The research in this paper contributes an evaluation of the dynamic characteristics of the runner of a hydraulic turbine unit, which is of great significance for the optimization of the analysis algorithm of the runner structure for large pumped storage units.