Recently, the competitiveness and innovation of science and technology have become an important index to measure the comprehensive ability of the country. Firstly, based on the respective theoretical origin, this paper uses the description statistical analysis method to analysis the capital structure and enterprise value of science and technology enterprises from 2012 to 2014. Then, identify the assets and liabilities rate, long-term debt rate, the correlation between the current debt ratio and corporate value through the regression analysis. Finally, according to the results of empirical analysis, the enterprise external financing environment and optimization of enterprise internal governance structure is proposed to maximize the enterprise value.