Storage allocation of outbound containers is a key factor of the performance of container handling system in automated container terminals. Improper storage plans of outbound containers make QC waiting inevitable; hence, the vessel handling time will be lengthened. A simulation-based optimization method is proposed in this paper for the storage allocation problem of outbound containers in automated container terminals (SAPOBA). A simulation model is built up by Timed-Colored-Petri-Net (TCPN), used to evaluate the QC waiting time of storage plans. Two optimization approaches, based on Particle Swarm Optimization (PSO) and Genetic Algorithm (GA), are proposed to form the complete simulation-based optimization method. Effectiveness of this method is verified by experiment, as the comparison of the two optimization approaches.