The concept of capital structure and corporate performance are first defined. Then the status and characteristics of the bio-pharmaceutical listed companies’ capital structure is analyzed by using descriptive statistical methods. It is found that a low level of overall asset-liability ratio, irrational debt structure are the characteristics of the capital structure of the bio-pharmaceutical listed companies from Shanghai stock exchange in China. And then a comprehensive evaluation of corporate performance of the bio-pharmaceutical listed companies is gotten by using Factor Analysis Method. Next the relationship between capital structure and corporate performance is studied empirically. At last, some suggestions are presented to optimize the capital structure of the bio-pharmaceutical listed companies in China to improve corporate performance.