The middle route of the south–north water transfer project (SNWTP) was built to relieve the pressure of increasing water demand in northern China. Serving as one of the major storage systems, optimal operation rules should be proposed promptly for Danjiangkou Reservoir, completed by a heightening project. In this paper, in order to seek out the optimal operation rules for Danjiangkou Reservoir, a multi-objective optimal operation model is developed, considering the inflow uncertainty, multi-year regulation cycle and water supply for the SNWTP. Three evaluation indexes (hydropower generation, water impoundment condition and shortage index) are adopted to assess the impacts of three influence factors (starting regulation level (SRL), inflow condition and flood control level) on Danjiangkou Reservoir operations. Finally, some critical operation strategies for Danjiangkou Reservoir are proposed. The results show that the optimal SRL for Danjiangkou Reservoir is 158 m and the recommended range of the water level at the end of the first year varies between 162–166 m (very wet), 164–166 m (wet), and 162–164 m (normal) on the basis of setting 158 m as the SRL.