Abstract: An Intelligent control can often be required for the multi-level canal systems in practical engineering, particularly with the increasingly large-scale irrigation districts in China. Nevertheless, most research can focus mainly on the single-level cascaded canal systems. Less attention has been paid to the simulation models and control algorithms of the multi-level canal systems. In this study, the Saint-Venant equations and the implicit finite difference algorithm were employed to establish a simulation model for the multi-level canal systems. The structures were also generalized, such as the inverted siphons and water diversion outlets. The HENRY formula was utilized to determine the relationship between the water levels of the main and branch canals and the flow rates at the water diversion gates. In the coupled control of the main and branch canals, a feedforward + feedback controller was adopted to control the openings of the regulating gates along the main canal and the water diversion gates at the heads of the branch canals. Among them, there were the consistence conditions of the water intake. The control algorithm was then optimized for the water diversion gates, according to the flow error threshold for the high stability of the diversion flow. Taking the Quanmutang Irrigation District Project as an example, the coupled model of the main and branch canals was verified to evaluate the channel’s response and the regulation of the gates. The results indicated that the main-canal-only model was basically consistent with the water level trend simulated by the coupled model of the main and branch canals. But there was a significant difference in the deviation amplitude of the water level. The water intake at the branch canals had a certain influence on the water levels of the main and the upstream canals. But there was a negligible influence on the water levels of the downstream main canals. The interval of the gate operations had a notable impact on the times of gate operation and the stabilization time of the water level. A large time interval reduced the times of gate operation by 41%, compared with a small time interval. The stabilization time increased by 157%. After setting a 3% flow error threshold for the optimized control algorithm of the water diversion gates, the number of gate operations decreased by approximately 77%, compared with the fixed time interval. The deviation of the water intake flow decreased by approximately 26%, compared with the static gates. This finding can also provide a strong reference to construct and control the complex multi-level models of the canal system.