Aiming at the problem of high inventory control costs of shipbuilding enterprises under uncertain conditions, this paper constructs and optimizes a dynamic collaborative replenishment model of shipbuilding enterprises inventory control. This model adopts integrated supply chain management theory and collaborative theory to analyze the inventory control principle in shipbuilding enterprises, and its goal is to minimize the cost and maximize the service level. The dynamic replenishment strategy from two types of suppliers is given by using mathematical knowledge, such as optimization theory, probability theory, and mathematical statistics to solve the model. Finally, shipbuilding enterprises take paint inventory control as an example to test and verify the validity and correctness of the model by using numerical simulation and sensitivity analysis. The results show that the dynamic collaborative replenishment model of shipbuilding enterprises inventory control can make full use of the advantages of two types of suppliers. Additionally, it cannot only quickly respond to demand changes, but can also maintain low operating costs. Therefore, the dynamic collaborative replenishment model could effectively solve the problem of high inventory control costs of shipbuilding enterprises under uncertain conditions and has great application value and practical significance.