This paper reviews the connotation of agricultural listed company and the related researches on capital structure theory of enterprises in China. Based on this, research hypothesis is put forward. Capital structure has positive correlation with the scale, growth and debt paying ability of agricultural listed company, and has negative correlation with the profitability, operating capability and cash capacity. Taking 37 agricultural listed companies as the research samples, a total of 15 financial indices reflecting the growth, profitability, enterprise scale, operating capacity, cash capability and debt paying ability are selected to conduct factor analysis. Based on the principle of eigenvalue greater than 1, five factors are ascertained, which can explain 84.04% variance of original independent variables. Factor loading matrix indicates that these five factors can be named as debt paying factor, profitability factor, scale and growth factor, operating capacity factor and cash capability factor. Multiple linear regression is carried out by taking factor score coefficient matrix as the independent variable, and asset-liability ratio of agricultural listed company as the dependent variable. Remove method is applied under 5% significant level. And only profitability factor can pass the test. Result shows that there is significant negative correlation between profitability and asset-liability ratio, which is inconsistent with the assumption and has supported the Pecking Order Theory. The other four factors have not passed the significant test, and have certain negative correlation with the capital structure of enterprises. Among them, correlation between the capital structure and the debt paying factor and scale and growth factor is inconsistent with the assumption. Combining with the analysis result, corresponding countermeasures for optimizing the capital structure of agricultural listed company are put forward.