The scheduling of docks and outfitting berths is crucial for shipyard operations, and the two are coordinated with each other, directly affecting shipbuilding efficiency and delivery time. To address this, a joint scheduling optimization model for docks and outfitting berths was developed, aiming to minimize the total ship delivery delay. To address the complexity and dynamics of shipyard operations, which involve various construction modes within the dock, ship section shifting, double-berth docking, and other intricate processes, a simulation-based optimization approach was proposed for solving the model. Case studies demonstrate that the proposed optimization model and simulation-based optimization method effectively optimize the joint scheduling of dry docks and outfitting berths, providing valuable insights for the scheduling and planning of shipyard resources.