This article used factor analysis to analyze microeconomic statistics of pharmaceutical industry in 13 prefecture-level cities of Jiangsu Province from 2011 to 2015. The innovation ability of pharmaceutical industry was evaluated and the features of those districts with innovation ability were concluded by cluster analysis. Disproportion in R&D financial input， R&D talents， policy environment and other factors among different regions resulted in disproportionate development in innovation ability of pharmaceutical industry. 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.