This paper analyzes the auxiliary decision-making modeling in the human resources of modern pharmaceutical enterprises based on the information system, introduces the development stage of business intelligence technology and human resource management, and explains why business intelligence technology should be introduced in the latest stage of human resource management. The application situation and market of foreign business intelligence are analyzed. Through the analysis of the current situation of the company's human resources development and the new requirements of human resources management in the new stage, the feasibility and necessity of the construction of the human resources auxiliary decision-making system are fully explained. At the same time, a comprehensive analysis of the company's actual human resources business was carried out to prepare for the implementation of the system design.