With the unfavorable navigation condition and complicated sailing environment, phenomenon like waterway block arises frequently in Yanshao waterway of Yangzhou segment. This article analyzes the main reason of waterway block and puts forward some corresponding countermeasures and a joint simulation scheduling model of multi-bottleneck is established at the same time. Besides, scheduling rules for vessels and evaluation criteria for this model are introduced in this paper. Furthermore, this model simulates ship operation and studies the effects of the improvement measures on Yanshao waterway of Yangzhou segment. Results show that, Yanshao waterway of Yangzhou segment is a multi-bottleneck nodes channel, Yan lock is the most critical factor in determining the overall through capabilities of Yanshao waterway. Vessels overtaking in the same direction and encountering in different direction at nodes are the primary causes of waterway block in Yanshao waterway of Yangzhou segment; optimizing management of vessels passing lock can reduce the phenomenon of waterway block. Simulation results prove that the joint simulation scheduling model of multi-bottleneck can optimize the management of vessels in Yanshao waterway, the cost-time of vessels in Yanshao waterway is rarely decreased despite, but the risk of channel congestion is reduced effectively, the latter has more guiding significant for scheduling in Yanshao waterway.