Currently, the food security situation is increasingly serious, and a growing number of food companies choose to implement the internationally accepted ISO9000 Series Standards. Based on the analysis of economic rationality and system drive for food enterprises to implement ISO9000 Series Standards, we determine the economic factors and institutional factors influencing enterprises' implementation of ISO9000 Series Standards, and establish corresponding indicator system. According to survey data on 86 enterprises in Sichuan Province, we draw the following conclusion using the Logit model: enterprise age and enterprise size in economic factors, government's food safety control intensity, consumers, public and media pressure, awareness of senior managers, strategic orientation of quality safety, employees' average educational level in institutional factors, have a significant effect on enterprises' implementation of ISO9000 Series Standards. According to research results, we put forth some recommendations for promoting food enterprises to implement ISO9000 Series Standards.