To evaluate the innovation ability of Jiangsu’s pharmaceutical industry and to provide theoretical support for the promotion of innovation ability of Jiangsu’s pharmaceutical industry. Methods: Develop an evaluation index system on the innovation ability of Jiangsu’s pharmaceutical industry, use factor analysis to analyze microeconomic statistics of pharmaceutical industry in 13 prefecture-level cities of Jiangsu province from 2011 to 2015, evaluate the innovation ability of pharmaceutical industry and conclude the features of those districts with innovation ability by cluster analysis. Results: Regional disparities exist in the innovation ability of Jiangsu’s pharmaceutical industry. Disproportion in R&D financial input, R&D talents, policy environment and other factors among different regions results in disproportionate development in innovation ability of pharmaceutical industry. Conclusion: To promote the innovation ability of Jiangsu’s pharmaceutical industry integrally, it is effective to set up trans-regional industrial cluster cooperation mode that accords with regional features, develop and improve R&D talent training mechanism, and strengthen the ability of learning and utilizing introduced technology.