On the basis of sorting the development of the theory of company performance evaluation, this study uses the VRS-DEA model and Malmquist index to evaluate the financial performance of 12 listed agricultural companies in China. Firstly, the selected sample data was standardized, and then the VRS-DEA model was used to analyze the financial performance indicators of the sample companies in 2019. Secondly, the financial performance indicators of the sample companies from 2015 to 2019 were used to longitudinally analyze the company's total factor productivity through the Malmquist index. Finally, based on the analysis of the financial performance evaluation results of sample companies, some suggestions for improving the financial performance of listed agricultural companies in China are put forward.