Improving innovation efficiency is of great significance to the sustainable development of the pharmaceutical manufacturing industry as well as the regional economy. To measure the efficiency of the innovation process from the perspective of the ecosystem, a model, including three head-to-tail stages, namely the innovative production process, innovative integration process, and innovative application process, is established. The DEA-Malmquist index is used to evaluate the static and dynamic innovation efficiency of the Chinese pharmaceutical manufacturing industry from 2009 to 2020. The results show that the overall innovation efficiency of the pharmaceutical manufacturing industry fluctuated, and the industry has not yet achieved steady growth in innovation efficiency during 2009–2020. Cross-sectional data comparisons found that there are significant differences in innovation efficiency among provinces. To improve the innovation efficiency of the Chinese pharmaceutical manufacturing industry, several suggestions are proposed, such as improving the technical efficiency, improving the efficiency of the whole process in innovative ways, and bridging the gap in innovation efficiency across regions. © 2022 by the authors.