During the process of switching conditions in pump-turbine, unstable flow would take place and seriously impact on the stability and safety. This paper deals with the guide vanes’ moving process in pump mode through unsteady numerical simulations. Dynamic mesh methodology is used for simulations in which GVO (Guide Vane Opening) from 9mm to 26mm. Simulation results approve that, there are many complex vortex structures and flow blockages phenomena under small GVO condition. Through the mathematical method of Fast Fourier Transform (FFT) and Short-Time Fourier Transform (STFT), the dominant pressure fluctuation frequencies are from runner blade passing frequency (BPF) and its harmonic frequency, as well as some other low frequencies are from unsteady flow states. Furthermore, the flow states are more unstable and complex under small guide vanes moving process. Compared with fixed GVO position, the flow states are more unstable and complex under guide vanes moving process, while the amplitude of main frequencies becomes higher.