The paper applied the Flexsim simulation software in pharmaceutical logistics industry in order to improve the operational efficiency of order picking process in pharmaceutical logistics center unbundled warehouse. Taking a large pharmaceutical logistics center as the research subject, according to the layout of unbundled warehouse, the simulation model was built with Flexsim simulation software, programmed with Flexsim script language and C language based on order picking process of unbundled warehouse. The simulation results were analyzed, the bottlenecks were identified, and the order picking process was optimized. The optimization results showed that the order picking time in unbundled warehouse was shorten and the efficiency of order picking operations was improved. The paper used the modeling and simulation methods to identify the bottlenecks of the order picking process, then optimized reasonably, thus improving the efficiency of order picking process in pharmaceutical logistics center unbundled warehouse.