This study aimed to analyze the time–frequency characteristics of pressure fluctuations and reveal their underlying flow mechanisms during the unavoidable guide vane closing process after a pump power-off in a pumped-storage hydropower plant. In this study, the weak compressibility model, one- and three-dimensional (1D–3D) coupling simulation method, and dynamic mesh technology were adopted simultaneously to accurately simulate the transient flow in a prototype pump turbine during the guide vane closure process after the pump power-off. According to the analysis results of the short-time Fourier transformation for the pressure fluctuations, apart from the familiar runner blade passing frequency and its harmonics, this study found a new component that is five times the runner rotation frequency as well as components that are lower than 4.5 times the runner rotation frequency and correspond to severe fluctuations in the pressure. Internal flow analysis suggests that the former is induced by unstable vortices near the trailing edges of the runner blades, whereas the latter ones are induced by local backflow vortices near the runner inlet. Additionally, these severe pressure fluctuation components were significantly large closer to the maximum reverse discharge of the pump brake mode. This finding indicates that these severe unsteady pressure fluctuation components can be suppressed by optimizing the reduction in the maximum reverse discharge in the pump brake mode.