For hydropower stations with sloping ceiling tailrace tunnel (SCTT), the regulation quality of hydro-turbine governing system (HTGS) under the proportional-integral-derivative (PID) strategy is poor. In order to improve the regulation quality of HTGS, the nonlinear disturbance decoupling control (NDDC) based on differential geometry theory is firstly applied into the HTGS with SCTT. The rigorous and complete construction method of nominal output function is proposed. Based on the obtained nominal output function, a novel NDDC strategy for HTGS with SCTT is designed. The application and performance of NDDC strategy on HTGS with SCTT are revealed. The results indicate that the regulation quality of the HTGS with SCTT under NDDC strategy is obviously better than that under PID strategy. The NDDC strategy has a favorable applicability on SCTT. The robustness of the HTGS with SCTT under NDDC strategy is excellent. In real engineering cases, the NDDC strategy can be adopted to optimize the design of the governor and improve the power supply quality of hydropower station.