A dynamic optimal allocation method for total amount control of water resources is proposed in this paper to determine the annual gross control index of water consumption and to rationally control water allocation according to inflow. With Fuhe River drainage basin as a case study, a model for optimal allocation of water resources is established with minimizing the water shortage in remaining stage (operation stage) as the objective, and water demand in water use area as well as flux requirements for control sections as constraints. The control index is real-time adjusted through the dynamic operation mode “forecast-decision-implementation-renewal”. Result shows that the water shortage rate in the water use area declines by 3.8%-25.3% when inflow scenario (IS) changes from wet to dry, while the water use in remaining stage is always controlled within the total amount control index when dry IS turns to wet. The annual total amount control index of water consumption calculated by the present method effectively adapts to different water conditions in the year, and meanwhile instigates or limits the supply of water according to different water supply conditions.