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The quality of agri-foods in e-supply chains confronts more threats than that in the traditional agri-food supply chain. However, most of the existing studies focusing on the quality problems of fresh agri-products are mainly cases studies and statistical analyses, and they do not take into account the farmers&rsquo, willingness to comply with safe agri-food supply procedures. To solve the supply quality problems of fresh agri-foods and help participators make a better choice, the decision-making behavior on the supply quality of agri-foods in the e-supply chain was deeply studied in this paper using game theory. Some factors related to the decision behavior of the supply chain were analyzed, including the supervision intension of the government, the rights protection consciousness of consumers, and the intensity of punishment for poor-quality agri-foods. These factors have an important influence on the farmers&rsquo, willingness to provide high-quality products and e-business&rsquo, probability of inspection. Compared with three different decision models of agri-food e-supply chains, the results show that the decentralized decision model is better than the centralized model from the view of quality protection. The behavior of members of the supply chain is as follows: the farmers&rsquo, willingness to supply high-quality agri-foods increases with the increase in the consumers&rsquo, consciousness of their rights and the government's supervision intensity. The &ldquo, experience deviation&rdquo, phenomenon also occurs when a new e-business makes a decision about its quality inspection behavior in this e-supply chain where the quality information is traceable. As such, e-business enterprises should reduce their quality inspection behavior based on the increase in the government's supervision intensity. This happens to be opposite to the traditional experience where quality information is not traceable. This study not only extends the research framework of the novel electronic supply chain, but also provides a certain reference for the subsequent research and e-business practices of fresh produce in developing countries.