Abstract: The rapid development of the pharmaceutical research and development (R&D) has brought new challenges to occupational health management, including the high uncertainty in the R&D process, emerging hazards, and compliance complexities associated with novel business models. Traditional management approaches exhibit limitations in effectively addressing the occupational health risks associated with these challenges. Based on the perspective of agile governance, this paper proposed an optimized pathway characterized by dynamic response, adaptive flexibility, and multi-stakeholder collaboration. It further offered countermeasures and recommendations from three aspects: concept renewal, mechanism innovation, and tool empowerment, aiming to provide reference for the effective management and control of occupational health risks in the innovation and development of the pharmaceutical R&D industry.