Based on the domestic and international studies about the profitability, this paper firstly introduces the general situation of the bio-pharmaceutical industry. Then the concept of profitability is defined. 78 bio-pharmaceutical listed companies from Shanghai stock exchange and Shenzhen stock exchange are chosen as research subjects. The comprehensive evaluation of the bio-pharmaceutical companies’ profitability from 2010 to 2012 is calculated by using factor analysis. Then this paper use regression analysis methods to study the factors that may affect the company’s profitability. Finally, combined with the analysis above, some suggestions are presented to improve the profitability of the bio-pharmaceutical listed companies in China.