Pump-turbine plays a significant role in the pumped storage station, and it is troubled by unreasonable hydraulic thrust. Some pressure balance devices have been adopted to ensure the safety of the pump-turbine unit, but the effect mechanism has not been numerical studied. This paper establishes the CFD model of the flow passage of a pump-turbine, wherein the crown gap, band gap, pressure balance pipe, and the discharge ostium are considered. Then, the flow characteristics of the pump-turbine at four typical operating conditions in turbine mode are calculated in transient scheme, and the numerical results agree with the experimental results. Finally, the effect of the pressure balance pipe and the discharge ostium on the pressure pulsation and the hydraulic thrust is discussed. The results show that the pressure balance pipe causes the direction of the axial hydraulic thrust to change from downward to upward, and the discharge ostium helps reducing the axial hydraulic thrust to a reasonable range. The pressure balance pipe and the discharge ostium have little effect on the radial hydraulic thrust. The pressure pulsation analysis provides a basis for revealing the mechanism of the hydraulic thrust frequency, and the rotor-stator interaction frequency exists in the axial hydraulic thrust. This paper provides a deeper knowledge of the impact mechanism of the pressure balance pipe and discharge ostium on the flow characteristics of the pump-turbine, which could contribute to future designs of the pump-turbine units, and is helpful for improving the safety of the pumped storage unit.