Uncertainties exist and affect the actual port production. For example, at the beginning of 2020, the sudden outbreak of COVID-19 seriously affected terminal production and increased the short-term pressure of handling at container terminals. Consequently, a large number of containers were stacked at terminals, and the problem of terminal congestion became more serious. To solve the congestion problem of container terminals and ensure the priority dispatch of emergency materials, this study uses the optimized arrival patterns of external trucks and a priority dispatch strategy for emergency materials to establish a bilevel optimization model for container terminals and proposes a chaotic genetic algorithm based on logistic mapping as a solution. Through numerical experiments, the algorithm proposed in this study was compared with the genetic algorithm and adaptive genetic algorithm. The experimental results show that the model and algorithm proposed in this study can effectively reduce the total cost of containers in a terminal while ensuring the priority dispatch of emergency materials, reducing the overlapping part of the time window, optimizing the arrival mode of external trucks, and reducing the waiting time of external trucks, effectively alleviating the terminal congestion problem.