Based on the theory of capital structure, the paper combines specification analysis with empirical analysis to discuss the factors which affecting the capital structure of the pharmaceutical industry and its influence. The essay constructs a panel data model to study the selected financial data of 119pharmaceuticallisted companies from 2010 to 2013. The results show that the size of enterprises and collateral value are positively related to capital structure; profitability, debt paying ability and ownership concentration are negatively correlated to the capital structure; development ability, tax shield effect of debt and operational ability are not significantly related to the capital structure. Finally, according to the current situation of the pharmaceutical regulation and the characteristics of pharmaceutical, this paper proposes some suggestions on how to optimize the enterprise’s capital structure.