In automated high-bay warehouses, the results of storage location allocation significantly impact the operational efficiency of subsequent warehouse operations. Considering that cargo loss within the warehouse is often caused by contact with equipment, this paper proposes an innovative dual-objective optimization model aimed at minimizing unit cargo loss and the average travel time of stacker cranes through rational storage allocation. The study’s findings indicate that different cargo sizes, shelf sizes, and operational modes have varying degrees of impact on stacker crane operational efficiency and cargo loss. A reasonable match between equipment and product sizes helps enterprises minimize space waste, expedite response to customer demands, and reduce operational costs. This study optimizes storage location allocation using the SPEA-II algorithm and performs a comprehensive comparison with the results from CPLEX and NSGA-II. The results demonstrate that the SPEA-II algorithm performs excellently across various problem scales, indicating that it is an effective method for solving storage location allocation issues.