Based on the arrival sequence and departure time of arrival trains, the container allocation optimization model of sea-rail intermodal import containers was constructed with the goal of minimizing the container overlapping amounts and the number of yard and bridge moving bays, and the correctness of model was verified by CPLEX. For the characteristics of the model and the problem, a heuristic algorithm was designed to solve large-scale real-world problems. Compared with the lowest stack stacking strategy, it was proved that the slot allocation optimization strategy can effectively reduce the overlapping amounts. On this basis, the influence of two factors, the size of operation box and the number of arrival trains on the optimization effect was analyzed. The results can provide theoretical support for the container allocation decision-making of sea-rail intermodal storage yard.