The internal flow field of the hydrogen circulation pump becomes more complex and flow process becomes more intense during the stopping process, strong vibration is generated to the pump and the working life of the pump is shortened. Therefore, the pressure pulsation at the inlet and outlet section, the radial force characteristics of the active rotor and the transient flow mechanism of the internal flow under different stopping modes are studied in this paper. The results show that the intake pressure and exhaust flow change greatly in exponential stopping mode, while the pressure pulsation amplitude decreases with the increase of stopping time in linear stopping mode. In addition, the radial force value of the active rotor in the exponential stopping mode is significantly smaller than that in the linear stopping mode, and the direction of the radial force Fx and Fy point to the negative direction of their respective axes.