Despite the pharmaceutical industry’s recognition of Industry 4.0, its full integration remains impeded by intricate technical, institutional, and regulatory challenges. To accelerate this transition, this work pioneers a concept of smart production-logistics synchronisation, leveraging the digital twin and innovative operations management strategy, for enhancing efficiency and sustainability in pharmaceutical manufacturing. A digital twin-enabled framework for transforming smart and sustainable pharmaceutical manufacturing is proposed. Following the framework, this paper presents an intelligent decision-making strategy by leveraging digital twin-enabled real-time information sharing and informed decision-making for synchronising production and logistics operations. A case study from a pharmaceutical manufacturer illustrates the potential benefits, with an average cutting of 18.60% in the production lead time, 67.31% in the logistics lead time, and 33.75% in the total energy consumption, respectively. Furthermore, the study demonstrates the resilience of the proposed strategy to logistics uncertainties, showcasing its effectiveness in mitigating delays and improving efficiency. These findings highlight the transformative potential of innovative operations management strategies enabled by industrial digital technologies in pharmaceutical manufacturing.