Relevant data ,from 145 pharmaceutical manufacturing listed companies in China from 2009 to 2014, was selected, a new indicator of effective tax burden (ETR) was adopted, which based on long-time cash flow data to measure the effective tax burden of these selected companies, and the differentiation was analyzed between specific pharmaceutical industries ,different regions and its variation trend. It shows that (1) from specific pharmaceutical industries, traditional Chinese medicine listed companies have the highest ETR, while medical equipment manufacturing limited companies have the lowest; (2) from different regions, those pharmaceutical manufacturing listed companies in the central regions have the highest ETR, while those companies in the eastern coastal regions have the lowest; (3) from variation trend, recently the pace of decline in the general ETR of pharmaceutical manufacturing listed companies in China has narrowed with an upward trend.