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This paper provides a mathematical model for Three Gorges-Gezhou dam co-scheduling problem, based on full analysis of Three Gorges-Gezhou dam’s actual needs, to maximize the total throughput of Three Gorges-Gezhou dam and the utilization ratio of shiplock area and minimize the total navigation shiplock waiting time under multiple constraints. This paper proposes a series queuing network (SQN) scheduling algorithm to divide the total ships that intend to pass through the shiplocks into four queues and calculate dynamically the weight of priority for each ship. The SQN scheduling algorithm schedules ships according to their priority weights which is determined by the characteristics of each ship, such as length, width, affiliation, waiting time, and so on. In the process, the operation conditions of Gezhou dam related to the navigable shiplocks and the task balancing among different shiplocks also should be considered. The SQN algorithm schedules ships circularly and optimizes the results step by step. Real operation data from our project shows that our SQN scheduling algorithm outperforms the traditional manual scheduling in which the less computational time is taken, the area utilization ratio of the five shiplocks is increased, the waiting time of high-prioritized ships is shorten, and a better balanced and alternating run-mode is provided for the three shiplocks in the Gezhou dam.