To research the flow capacity changes of the Middle Route of South-to-North Water Diversion Project, a composite roughness coefficient calibration model was established to analyze the overall pattern of the composite roughness coefficient and its impact on the flow capacity based on the observation data of water level and discharge in the main canal from 2019 to 2023. The results show that there are differences in the composite roughness coefficient of each section along the main canal, and the composite roughness coefficient is higher in the upper reach than that in the lower reach, with the mean values of 0.0168 and 0.0157, respectively. The composite roughness coefficient of the canal may gradually increase with the running time, and the value could be reduced by appropriate engineering maintenance or reconstruction measures. The increase of the composite roughness coefficient of the canal causes a change in its flow capacity. The water level upstream Zhanghe inverted siphon section, with a range about 456km in the middle route exceeds the design value when transporting the designed flow in the main canal. To ensure the safety running of the project, some countermeasures are proposed, including systematically exploring the influence mechanism and potential tapping measures of the flow capacity of the main canal, timely carrying out the water delivery test with enlarged discharge through the main canal, and establishing a real-time prediction system of the composite roughness coefficient in canals. Keywords: composite roughness coefficient; flow capacity; water transport safety; the Middle Route of South-to-North Water Diversion Project 〖FL