As a fundamental and strategic industry that safeguards people’s life and health, the pharmaceutical industry plays an irreplaceable role in building a strong public health security barrier, enhancing the core competitiveness of national industries, and strengthening the self-reliance and controllability of the innovation chain, industrial chain, and supply chain of a country. Against the background of accelerating the construction of a manufacturing powerhouse and Healthy China, together with the transformation of China’s pharmaceutical industry from scale-led development to innovation-driven growth, it is urgent to summarize the innovative development achievements of China’s pharmaceutical industry and forecast its future development layout. Over the past decade, the scale of China’s pharmaceutical industry has first expanded and then stabilized, its profitability resilience and export delivery value have continued to improve, internationalization has become increasingly diversified, and institutional mechanisms and policy systems have continuously improved. Cutting-edge technologies of China’s pharmaceutical industry have developed rapidly with accelerated innovative application and iterative upgrading, driving the industry’s development model to shift from scale expansion and generic follow-up to quality leadership and global innovation. A full industrial chain layout of the industry has been formed, the international competitiveness of leading enterprises in the industry has been significantly enhanced, and regional innovation has achieved differentiated development. Focusing on industrial scale, innovation chain, and industrial chain, this study analyzes the development trend of China’s pharmaceutical industry, and discusses its development opportunities and challenges as well as the 2035 development vision. Furthermore, future layout directions of China’s pharmaceutical industry are analyzed, including an innovation chain layout centered on cutting-edge technologies and key industrialization technologies in the pharmaceutical industry; an industrial chain layout focused on addressing shortcomings in the upstream, midstream, and downstream sectors and constructing regional innovation centers; an digital chain layout dominated by the promotion of cutting-edge technologies and the construction of pharmaceutical industry data platforms; and a policy layout with institutional innovation and the improvement of policy support systems as the core.