In order to make the runoff close to the natural state and make the change of ecological flow within the acceptable range, by setting appropriate upper and lower limits of ecological flow and considering the ecological overflow and water shortage rate as well as the comprehensive water shortage rate as targets, an ecological scheduling model in reservoir group operation of Zhuozhang river basin was established. This model was solved according to the large-scale system decomposition-coordination technology and DP method. The difference between results with the minimum ecological overflow, water shortage rate and the minimum ecological water shortage rate was compared and analyzed. The results verified the effectiveness of system coordination. Within the capacity of reservoir regulation and storage, the model solved the imbalance of inter-annual water shortage in time and completed the ecological water supply task jointly undertaken by the downstream in space. Taking the minimum ecological overflow and water shortage rate as the ecological target, the lower monthly average water shortage rate and higher ecological satisfaction degree can be obtained compared with the traditional minimum ecological water shortage rate. The monthly average water shortage rate of Zhangze, Houwan and Guanhe reservoirs was reduced by 0. 25%, 0. 62% and 0. 03% respectively, and the annual average ecological satisfaction degree was increased by 2. 5%.