The work aims to simulate the operations of stereoscopic warehouse of pharmaceutical logistics center with Flexsim, in order to shorten the time of out-put and in-put warehousing of stereoscopic warehouse and optimize the combination of personnel and equipment during the operation. Taking a large-scaled pharmaceutical logistics center as the research object, according to the actual layout of stereoscopic warehouse, a simulation model was built with Flexsim simulation software. First, genetic algorithm was used to determine the optimal out-put and in-put sequence, and the results were simulated in the Flexsim which could prove the practicability of the algorithm. Then, the whole process of stereoscopic warehouse was simulated. The efficiency of out-put and in-put warehousing was improved by 12.4% and the warehousing that enabled the optimal use of personnel and equipment to be achieved under the configuration of (2,2,2,2) was established. With modeling and simulation, the bottlenecks of the process are identified, the optimal out-put and in-put warehousing sequence and combination of personnel and equipment are confirmed, the efficiency of out-put and in-put operation in pharmaceutical logistics center is improved, and the costs of equipment and personnel are reduced.