In recent times, optimization began to be popular in the turbomachinery field. The development of computational fluid dynamics (CFD) analysis and optimization technology provides the opportunity to maximize the performance of hydro turbines. The optimization techniques are focused mainly on the rotating components (runner and guide vane) of the hydro turbines. Meanwhile, fixed flow passages (stay vane, casing, and draft tube) are essential parts for the proper flow uniformity in the hydro turbines. The suppression of flow instabilities in the fixed flow passages is an inevitable process to ensure the power plant safety by the reduction of vortex-induced vibration and pressure pulsation in the hydro turbines. In this study, a CFD-based shape design optimization process is proposed with response surface methodology (RSM) to improve the flow uniformity in the fixed flow passages of a Francis hydro turbine model. The internal flow behaviors were compared between the initial and optimal shapes of the stay vane, casing, and the draft tube with J-Groove. The optimal shape design process for the fixed flow passages proved its remarkable effects on the improvement of flow uniformity in the Francis hydro turbine.