The container terminal handling system plays an important role in marine transportation, and improving its efficiency has become a big challenge. Therefore, this paper proposes an analytical method that combines a Petri net with simulation tools. Firstly, the container terminal handling system is abstracted into a Petri net system according to the internal logic of the handling process. Next, eigenvalues of the correlation matrix are calculated to analyse the effectiveness of the Petri net system. Then, the Petri net system is simulated using the Extend-Sim software. The result suggests that, after optimising, the handling capacity of the berth is clearly improved. Using the Petri net and simulation tools together to analyse the container terminal system is the innovation and the most important aspect of this paper. Because the combination of a Petri net and simulation can not only ensure the reliability of the model but also optimise the container terminal handling system more intuitively.