The innovation and development practices of the pharmaceutical industry are of great importance for the continual enhancement of public health. Industrial clusters are one of the important means by which the pharmaceutical industry can be transformed and developed, but there is a lack of research on the evolutionary path and development innovation of pharmaceutical industrial clusters. As a country with a major pharmaceutical industry, the transformation and development path of traditional pharmaceutical industrial clusters in China has important reference value for the sustainable development of the global pharmaceutical industry. Through an analysis of the evolution of traditional pharmaceutical industrial clusters in Shijiazhuang, this study explores the law of the dynamic evolution of pharmaceutical industrial clusters and the associated mechanisms. Specifically, we conclude that the evolutionary path of traditional pharmaceutical industrial clusters can be divided into the government-led pharmaceutical industrial cluster start-up stage, the government-guided pharmaceutical industrial cluster development stage, and the government-served pharmaceutical industrial cluster transformation stage. The operating mechanisms include a self-organization mechanism, an innovation-driven mechanism, and an outward associated mechanism, each of which plays different roles in the different stages of the dynamic evolution of the cluster, and the synergistic operation of the three mechanisms forms an important basis for the evolution of pharmaceutical industrial clusters. We found that the innovation development of traditional pharmaceutical industrial clusters is influenced by the synergy of the self-organization, innovation-driven, and outward associated mechanisms. The self-organization mechanism is a necessary condition for pharmaceutical industrial clusters to realize the transition from disorder to order. The innovation-driven mechanism is the core driving force for the innovative development of pharmaceutical industrial clusters. Finally, the outward associated mechanism is the main means by which pharmaceutical industrial clusters integrate into the global value chain.