Abstract: As the core node of the intermodal container transport network, the operation efficiency of the container multimodal port is directly related to the passing efficiency of the entire intermodal transport network, and the operation efficiency of the storage yard is particularly important to ensure the overall efficiency of the port. In the actual operation of the port, the reasonable space allocation of containers waiting for loading based on the ship stowage plan can effectively improve the operation efficiency of the storage yard. Under the background of container multimodal transport, the space allocation of container in storage yard is studied by considering the ship stowing plan, taking the containers waiting to be loaded in highway, railway and waterway port as the object and combining with yard bridge operation. In order to ensure the overall operation efficiency of the container yard, a two-stage mathematical model of minimum turnover and minimum operation time of the yard bridge was established, and the artificial bee colony algorithm was improved to solve the problem. In order to avoid the influence of two-stage solution on the global optimal, the optimal scheme is obtained by the coordination of pheromone and sensitivity to balance the two-stage optimal solution. The results show that the improved artificial bee colony algorithm is better than the general artificial bee colony algorithm and genetic algorithm in terms of yard turnover and bridge operation time. With the increase of the scale of the example, the advantages of the improved artificial bee colony algorithm are more prominent, and the solution quality and efficiency are the best. The results above demonstrate the effectiveness of the model and algorithm, and have a certain reference significance for the actual development of storage yard space allocation plan.