OBJECTIVE：To provide reference for optimizing resource allocation and precise investment of China ’s pharma- ceutical industry. METHODS ：The number of invention patent applications in China ’s pharmaceutical industry was searched from China Intellectual Property Netwerk ，and the status quo and structure of patent applications in China ’s pharmaceutical industry were analyzed. SPSS 23.0 software was used to analyze the input-output correlation of the number of invention patent applications with R&D investment and main business income of pharmaceutical enterprises in China. RESULTS ：The number of invention patent applications in China ’s pharmaceutical industry increased year by year. From 2000 to 2015，225 861 invention patents had been applied by domestic applicants and 43 149 invention patents had been applied by foreign applicants in China ；only 49.94％ domestic applicants applied for professional invention ，while 96.79％ of foreign applicants applied for professional invention. There was a positive correlation between the R&D expenditure of pharmaceutical enterprises and the number of invention patent applications，which indicated that the R&D investment of pharmaceutical industry in China was beneficial to the invention patent applications. The number of invention patent applications of pharmaceutical enterprises was also positively correlated with the main business income ，indicating that the increase of invention patent applications of pharmaceutical enterprises also effectively expanded the economic scale of pharmaceutical industry. CONCLUSIONS ：Compared with foreign countries ，the structure of patent applicants in domestic pharmaceutical industry needs to be adjusted urgently. Pharmaceutical enterprises have not yet become the main applicants. The continuous R&D investment of pharmaceutical enterprises effectively promotes the application of invention patent，expanded the economic scale of the pharmaceutical industry.