Abstract: The digital transformation of pharmaceutical industry is the comprehensive result of multiple policies, such as the drug safety traceability management, post-marketing changes, data management requirements, and integration of industrialization and informatization, which can reduce costs, improve quality, increase efficiency, and promote the drug risk management capabilities. Based on analysis of the pharmaceutical information situation, institutional environment, and the digital technology application, the digital transformation business environment of domestic pharmaceutical industry has been optimized. The digital transformation of the pharmaceutical industry inevitably involves the technological transformation of process changes. The empirical analysis result showed that the best path was to integrate digital technological transformation from the new pharmaceutical innovation stage. The application of the change system in the digitalization of enterprises after the listing of the pharmaceutical industry was analyzed, the three-dimensional structure system framework of the pharmaceutical information engineering construction, drug quality management process and pharmacovigilance was designed and constructed. The framework is composed of four transformation elements of data, technology, business process and organizational structure, and three transformation processes of informatization, digitization and intelligence. Finally, the pharmaceutical transformation and upgrading paths were proposed, such as the supervision informatization, digital design selection, third-party services, and the departmental coordination mechanisms, with a view to providing reference and suggestions for future research.