Ultra-high head pumped-storage units (PSUs) have longer upstream and downstream pipelines and more complex internal flows than those of conventional head units. This complexity increases the difficulty of simulating transient flows in ultra-high head pump-turbines (PTs). When numerically studying the transition process of an ultra-high head PSU, determining accurate time-varying boundary conditions and analyzing complex pressure pulsations is crucial. In this study, one- and three-dimensional (1D-3D) coupled computational approach was employed to simulate the turbine runaway process (TRP). The short-time Fourier transform (STFT) method was used to analyze the time–frequency characteristics of the transient pressure, revealing the formation mechanism of each pressure pulsation component. In addition to the pressure pulsation components that occur during the TRP in conventional head PTs, a novel pressure pulsation component was revealed. This component, extended from low frequency to high frequency and had a higher amplitude at 25 ∼ 27 times the rotational frequency, was induced by transient flowrate pulsations. This could significantly exacerbate the pulsation of the axial force. The findings provide a reference for the subsequent research and development of ultra-high head PSUs.