The units of pumped-storage power station always have a serious instability when the pump turbine working at transition process of turbine mode. Both the steady and unsteady numerical simulation were carried out to simulate the inner flow in pump-turbine. When considering and not considering the weak compressibility of water respectively, the internal flow field of two kinds of turbine operating mode and pressure fluctuation of a small opening condition of turbine operating mode are analyzed. The results show that the ″water seals″, a plurality of annular flow area which appeared in vaneless zone, under the small opening during turbine mode and those water seals blocked infiow from the guide vane domain. A pressure pulsation, which dominant frequency is 7fn, has emerged in the vaneless space under the small opening condition during the turbine mode. The amplitude of the pressure pulsation of the case which considered the compressibility is slightly larger than the others. Additionally, a pressure pulsation, dominant frequency is rotating frequency, has occurred in draft tube. And this pressure fluctuation is related to the structure of spiral vortex. Furthermore, when the compressibility is considered, there is a pressure pulsation occurred at the main frequency of 10fn in the draft tube. Meanwhile, the spiral vortex zone becomes heavier.