The method of water supply operation for Danjiangkou Reservoir is important for getting more benefit by South-north water diversion project in the middle line. The key of this method is to control water supply of each object so as to balance the demand between water resource area and water-receiving area, as well as give full play to the key role of controlling reservoirs. It is necessary to put forward an effective scheme to meet the requirement of operation under water shortage of South and North. In this paper, a water supply declining control scheme under water shortage of South and North is proposed based on the analysis of present situation. The research of influence by initial water level is implemented to find the warning water level. The water supply declining control scheme under water shortage of South and North is proposed and the corresponding results are calculated. The results of this study can be used for making the operation scheme of Danjiangkou Reservoir in the middle route in the south-to-north water diversion project.