Abstract: The method includes: S1: formulating a layered game architecture for a port-and-ship integrated energy and transportation operation; S2: establishing a port-and-ship layered game optimization model based on an optimized objective function and an optimized constraint condition of a port and an optimized objective function and an optimized constraint condition of a ship; and S3: based on the port-and-ship layered game optimization model, solving, by the layered game architecture, an optimal integrated operation method for the port-and-ship energy and transportation system through a KKT (Karush-Kuhn-Tucker) optimality condition solving method. The port-and-ship layered game optimization model means that the port, as a superior guider, formulates and executes a strategy, the ship, as an inferior follower, makes corresponding responses by taking the strategy formulated by the port as a constraint, and the ship updates its strategy according to the responses made by the ship till reaching a game equilibrium.