This paper is related to the deign optimization of axial flow hydraulic turbine runner. An improved Q3D inverse method has been proposed from the system point of view, and a set of rotational flow governing equations as well as an equation for blade geometry design have been derived. The computation domain is firstly taken from the inlet of the guide vane to the far outlet of the runner blade, and flows in different regions are solved simultaneously. Therefore, the influence of wicket gate parameters on runner blade design is considered and the difficulty of defining the flow condition at the runner blade inlet is overcomed. Because a pre-computation of initial blade on the S₂m surface is newly adopted, the iterations of S₁ and S₂m surfaces has been greatly reduced. Experimental results have validated the present model and a direct flow analysis has demonstrated the reliability of the inverse computation. Numerical investigations show that the effect of wicket gate parameters should be considered also in runner design.