The hydraulic turbine in turbine mode (TMHT) with ultra-low specific speed is a new type of energy recovery device for recovering energy stored in the high-pressure fluid. In order to solve the problem of insufficient consideration of runner geometric parameter optimization, this paper proposes an optimization strategy (OT-CFD), which is based on the orthogonal test method and computational fluid dynamics (CFD), to optimize the performance of the TMHT runner. Firstly, the orthogonal test schemes are established with 5 levels of runner inlet diameter, outlet diameter, inlet height, blade inlet angle, and blade number. Then 25 three-dimensional models of two-stage TMHT containing flow passage components such as Francis runner are built. Further, the internal flow characteristics and energy characteristics of TMHT are calculated and then verified by the real machine test. By comparing the numerical simulation results, the design schemes of runner geometry parameters corresponding to the highest head (H) and the highest efficiency (η) are determined, respectively. On this basis, the optimization effect of runner geometry parameters is analyzed by numerical simulation based on CFD. In conclusion, the inlet angle is the most important factor affecting the efficiency, and the runner inlet diameter is the most important factor affecting the water head. Compared with the comparison scheme, the optimal η scheme has a more stable flow pattern, which provides an efficiency increase of 10.9%, a water head increase of 26.75 m, and a power increase of 646.32kW, greatly reduces the energy loss in the process of residual pressure recovery; the optimal H scheme has an efficiency increase of 2.61%, but more stable and regular flow pattern. More importantly, the optimal water head scheme, which has a water head increase of 185.53 m and a power increase of 1518.3kW, greatly increases the capacity of recovering the water head.