According to the investigation results of 70 green food enterprises in Sichuan Province, the strategic targets of enterprises implementing green food certification are discussed by borrowing ideas from the Balanced Score Card. Balanced Score Card index system is selected and improved according to the changes of enterprises before and after implementing the green food certification system. Then, the performance evaluation index system of enterprises implementing green food certification is established. This index system has five strategic directions of finance, customer, internal management, social ecology, and learning and growth, and has 11 strategic targets, such as increasing operating profit, expanding market, improving the quality of staff, improving the production technology level, enhancing the core competence of enterprises, ensuring food safety, improving the physical quality of human, and protecting ecological environment. According to the principles of guidance, scientificity, comparability, feasibility, and significance, a total of 24 evaluation indices are established, including the change of product cost, change of product sales revenue, change of profit rate, change of return on investment, change of internal and external lost cost, change of the proportion of certified products in total sales and so on.