Abstract: Since 2012, the joint operation program of water projects for Changjiang River basin has been prepared year by year. Combined with the continuous in-depth research results, the joint operation program has been continuously expanded and updated with more water projects involved and optimized operation methods. It has become the key non-engineering measures for real-time flood management of Changjiang River Basin. In 2020, Changjiang River experienced large river basin floods, the third largest flood only less than 1954,1998. Under the guidance of the basin joint operation program of water projects, and based on the flood characteristics and flood control situation, the Three Gorges Reservoir played a core role, and jointly operated with various types of water projects such as the reservoirs from upper and middle streams areas, the floodplain areas, the drainage pumping stations, and the detention basins etc. The joint operation of all types of water projects had successfully mitigated flood risks of the 5 numbered floods in 2020, and had significantly reduced flood damage. However, during the management practices, it found that due to the changing environments, particularly the completion and commissioning of controlling water conservancy projects in the river, the significant improvement of flood drainage system along the river, the social and economic development of the floodplain areas especially in the detention basins, and the changes of river morphology and flood routing characteristics, the joint operation program of water projects that was developed based on designed flood events, could hardly cover the full combinations of hydro-meteorological conditions and flood characteristics which were far more complicated than the designed floods. In 2020 flood management practices, the joint operation program had been applied but with various modification according to real-time management needs. The paper analyzes the operation scheme and the effects of the application of the joint operation of water projects, special attention is paid to the difference between the joint operation program and the actual operation. Discussions and suggestions are made on further improvement of the joint operation program of water projects of Changjiang River Basin.