In twenty-first century, automated stereoscopic warehouse has attracted many attentions of the enterprises because it has high working efficiency. The operation efficiency and management benefit of an automated stereoscopic warehouse are affected directly by the order picking efficient, it is an important symbol of service level about the automated stereoscopic warehouse. This paper from the perspective of the warehouse management to discuss the issue, the optimization assigned of location selection is regarded as the ultimate goal. A multi-objective mathematical model is established by setting “job efficiency” and “turnover rate” as objective functions, “warehouse space layout” as the constraint condition, and the genetic algorithm is used for coding this mathematical model which is applied to a pharmaceutical warehouse and solved by using Matlab software, result shows that the picking efficiency of normal temperature zone and the turnover of cargo area are have been greatly improved.