The scheduling of the Gezhouba Hydropower Station is challenged by the uncertainty of the changes of downstream water level, as it is susceptible to backwater effect caused by the inflow from the Qingjiang River. In order to identify the impact of the backwater effect on the Gezhouba Hydropower Station scheduling strategy, we analyzed the extent of the backwater effect of the Qingjiang River inflow on the Yichang Hydrological Station based on the monitored hydrologic data, and in turn identified the loss output of the hydropower station. Results show that the backwater effect of the Qingjiang River inflow on Yichang Hydrological Station increased with the increase of the inflow, but decrease with the increase of the water flow in the Yichang Hydrological Station. Meanwhile, the loss output of the hydropower station increased with the increase of the inflow, whereas experienced increase-to-decrease transition with the increase of the discharge flow, and reached its maximum when the discharge flow was at full capacity. Study results is conducive to the decision-making of scheduling strategies for the Gezhouba Hydropower Station. However, the actual formulation of its scheduling strategy should take the joint regulation of the Three Georges Reservoir and optimization of water level control into consideration.