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To improve the efficiency of tier-to-tier shuttle-based storage and retrieval system (SBS/RS), the optimization problem of the location allocation based on the mixed storage of goods is proposed. Considering the effect of warehouse operation scheduling and batch outbound allocation on the location allocation, an optimization model with the shortest outbound time of all outbound orders in a certain historical period is established. The optimization model consists of two stages: location allocation and job scheduling. A two-layer genetic algorithm is designed to solve the model. The first layer is used to solve the location allocation, and the coding method is group coding; the second layer is used for job scheduling, and the coding mode is real number coding. When the population is initialized during the location allocation phase, the BFD algorithm is used to improve the convergence velocity of the algorithm. Taking the actual data of a tier-to-tier SBS/RS of an aviation food company as an example, the established model and design algorithm were verified, and the different batch intervals of each cargo space for storing different types of goods and outbound were analyzed. The optimization effects of the algorithm are compared, and the effects of considering the job scheduling and not considering the job scheduling on the location allocation are compared. The results show that based on the cargo allocation strategy of cargo mixed storage, the outbound efficiency can be improved by about 20%. Considering job scheduling, the efficiency of warehousing is improved by about 5% compared with the optimization of warehouse allocation without job scheduling, where the efficiency of delivery is increased by about 6%.