The aim of this work was to study the optimization of storage spaces in regional distribution centers of retail chains under the partition picking system. This paper took a pharmaceutical retail chain enterprise RDC as the object of study, set the zoning time balance as the goal of storage space optimization, established a mathematical model and used the genetic algorithm to achieve the solution in order to improve the efficiency of distribution center selection. Under the premise of sample orders accounting for 80% of the weight, comparing the chosen status of the study object with the picking time corresponding to the partitioning result and the storage location solved, we found that the solution based on the balancing picking time of different partition model increased by 37.34% in efficiency compared with the results, and the optimization effect was obvious. In conclusion, empirical studies have shown the effectiveness of the model and algorithm, and the optimization method is also widely applicable in the allocation of storage spaces in other partition picking systems.