High amplitude of pressure fluctuation is observed in a draft tube of a hydraulic turbine and a pump-turbine, for the case of partial load operation. Several methods had been reported to mitigate the amplitude so far, such as, air or water injection to the draft tube, fins on the draft tube surface, or runner replacement with optimized velocity profile at runner exit. However, several problems for each method can be considered, such as, negative influence on efficiency, high cost, technical difficulties for installation, and so on. To solve these problems and satisfy the demand for mitigating the amplitude of pressure fluctuation simultaneously, a new runner cone with spiral grooves on the surface was developed. It was developed with unsteady draft tube calculation based on Design of Experiment (DOE) method, and the effect was confirmed by model tests. Finally, developed runner cone was installed to the prototype pump turbine, and predicted performance was confirmed by on-site tests. However, the reason why the grooved runner cone can mitigate the amplitude of pressure fluctuation in draft tube was not clarified. Therefore, numerical investigation focusing around runner cone was carried out. As a result, it was clarified that the velocity profile at runner outlet was modified by the grooved runner cone, such as, reverse flow downstream of runner cone and tangential velocity was reduced. It means the shear stress between main stream and dead water core region was weakened, therefore, it can be estimated that the amplitude of draft pressure fluctuation was reduced.