The Pump-As-Turbine (PAT) technology has become popular in micro hydropower stations due to its simple installation and cost-effectiveness. Nevertheless, power failures present a substantial risk to the secure and steady functioning of PAT’s braking system. The commercial CFD code (ANSYSCFX) is improved by incorporating a secondary development to model the power-off transition using Fortran accurately. This enhancement allows for real-time iterative calculations of angular momentum equations for mixed-flow PAT at different speeds. Meanwhile, the time-frequency domain analysis is utilized to analyze pressure pulsation signals and the evolution of the internal flow field in mixed-flow PAT. An investigation was conducted to have a deeper understanding of braking circumstances. The results revealed that the main frequency of the pressure pulsation aligns with the blade frequency at various flow rates, and there is a sudden change in pressure amplitude during the braking phase. The impeller experienced the majority of energy losses, with the draft tube being the subsequent area of concern. In addition, a thorough examination and comparison of the changes in the internal flow field during braking were carried out. This analysis revealed a distinct double helix structure within the draft tube, with a slower inner helix and a faster outer helix. Furthermore, it was observed that there is a strong correlation between wall shear stresses and hydraulic losses on the blade surface. This research enhanced understanding of the flow characteristics of mixed-flow PAT can help improve system safety and provide valuable guidance for future optimization efforts.