OBJECTIVE：To provide refer ence for improving the innovation efficiency of Chinese pharmaceutical industry and promoting the high-quality development of the pharmaceutical industry. METHODS ：Using local economic development ，policy support，industrial foundation and innovation foundation as environmental variables ，three-stage data envelopment analysis （DEA） was used to explore the change regularity of innovation efficiency of the pharmaceutical industry by collecting related data such as input，output and invironment of 31 provinces（autonomous regions ，municipalities）in China during 2012-2016 and in 2018 from China Statistical Yearbook and China High-tech Industry Statistical Yearbook . RESULTS & CONCLUSIONS ：The innovation efficiency of the pharmaceutical industry in 18 provinces（autonomous regions ，municipalities）were overestimated ，and other 13 provinces（autonomous regions ，municipalities）was underestimated. The innovation efficiency of Fujian ，Heilongjiang，Jilin， Jiangxi，Yunnan，Liaoning and Chongqing before adjustment were overestimated 0-0.1，Shaanxi，Hainan，Gansu and Shanxi were overestimated 0.1-0.3，Inner Mongolia ，Guizhou，Guangxi，Xinjiang and Ningxia were overestimated 0.3-0.5；while the innovation efficiency of Anhui ，Hunan，Shanghai，Beijing，Hebei，Sichuan，Tianjin and Henan were underestimation 0.1-0.3，Hubei， Jiangsu，Zhejiang，Shandong and Guangdong had an underestimation of 0.3-0.5 before adjustment. Tibet ，Qinghai and Guangdong were greatly affected by environmental factors. The innovation efficiency in Tibet and Qinghai before adjustment were overestimated by 0.603 and 0.538 compared with after adjustment ，while Guangdong was underestimated by 0.470. The innovation efficiency value of the eastern and central regions of China before adjustment was underestimated ，while the northeastern and western regions were overestimated overall. B efore the adjustment，the order of innovation efficiency in descending order was the central ， western， eastern and northeastern liying@163.com regions，and after the adjustment ，it became the eastern ，central， northeastern and western regions. The innovation efficiency of Chinese pharmaceutical industry is greatly affected by the environment ，so all localities shou ld pay attention to the po licy support for the pharmaceutical industry and strengthen the policy guiding role for the pharmaceutical industry ；improve the industrial chain and supporting measures to create a good innovation environment ；promote the flow of innovation resources in different regions ，strengthen the cooperation and exchange among regions ，so as to improve the innovation efficiency of Chinese pharmaceutical industry and promote the high-quality development of the pharmaceutical industry.