The start-up process of a pump-turbine in pump mode is found with obvious noise, especially at the small guide vane opening angle. The turbulent-flow-induced noise is an important part and must be reduced by flow control. Therefore, the computational fluid dynamics (CFD) method is used in this study to predict the internal flow in a high head prototype pump-turbine (the specific speed nq is 31.5) under an extremely off-design condition (Cφ = 0.015 and Cα = 0.096). The acoustic analogy method is also used to predict the near-field noise based on the turbulence field. Special undesirable flow structures including the flow ring between the runner trailing-edge and the guide vane, guide vane jet, twin-vortexes adjacent to guide vane jet, inter stay vane vortex, stay vane jet, and volute vortex-ring are found in a pump-turbine. These complex jet-vortex flow structures induce local high turbulence kinetic energy and an eddy dissipation rate, which is the reason why noise is generated at small guide vane opening angle. Three dominating frequencies are found on the turbulence kinetic energy pulsation. They are the runner blade frequency fb = 64.5 Hz, the dominate frequency in the guide vane and the stay vane fgsv = 9.6 Hz, and the dominate frequency in volute fvl = 3.2 Hz. The flow pulsation tracing topology gives a good visualization of frequency propagation. The dominating regions of the three specific frequencies are clearly visualized. Results show that different flow structures may induce different frequencies, and the induced specific frequencies will propagate to adjacent sites. This study helps us to understand the off-design flow regime in this prototype pump-turbine and provides guidance when encountering the noise and stability problems during pump mode’s start-up.