Shipping intelligent management decision system is the basis of ship operation management. This paper focused on the key decision-making links in shipping operation management: ship risk prediction, optimization and control. In this paper, the research status and existing problems were analyzed, and the ship dispatching decision-making optimization model was deeply studied. This can better solve the problem of shipping risk assessment and decision-making in the process of ship dispatching, and provide decision-making basis for the management of shipping enterprises. The research contents of this paper include: (1) the overall structure of ship operation management decision system is proposed in this paper. This paper first analyzed the design requirements of the ship operation management decision system, and then described the construction process of the shipping intelligent management decision system in detail. (2) Based on Bayesian network, this paper established a ship intelligent management decision system. Finally, this paper verified that the accuracy of the shipping intelligent management decision system based on Bayesian network Model was 29% higher than that of the Structural Equation Model (SEM).