Hydraulic turbines are usually required to operate in a wide range. The operation at off-design conditions not only reduces the unit efficiency, but also significantly deteriorates the dynamic stability of the turbines. In order to develop a turbine runner with good performances under multi operation conditions, a comprehensive hydraulic improvement has been done of a Francis turbine runner with a multipoint and multi-objective optimization design system. Compared with the initial runner, the runner generated from this method has a satisfactory improvement. In detail, unit efficiencies of the preferred runner are increased by 0.91%, 0.47% and 0.37%, respectively, under the rated head, a high head and the maximum head. The lowest pressure at blade surface is improved by 376.2 kPa under the rated head. CFD calculations are conducted to analyze the flow conditions inside of the preferred runner. In addition, runners with different main design inputs, namely blade lean, blade loading and blade meridional shape are furtherly investigated to reveal their relationship with runner’s internal flow and outer performances. In description, this optimization system supplies satisfactory results and convincing recommendations to determine the design inputs for low-head Francis turbine runners.