In recent years, a series of pesticide poisoning scandals have hit the Chinese agri-food industry and weakened consumer confidence on agri-food and peasants. Considering that peasants are the key producers in the agri-food production, we explore how peasant behaviour is shaped in the contemporary Chinese agri-food system. Based on field surveys in Henan province and previous studies, we simplify the complex agri-food system into three supply models, the “wholesale market-centred” model, the “leading enterprise-centred” model and the “farming-supermarket docking” model, in order to manifest the conventional agri-food supply mechanism. We develop the concept, “peasant niche”, to describe the position and situation of peasants in each model. We argue that with little autonomy and heavy dependence on other actors including wholesalers, leading enterprises and supermarkets, the peasant niche in the three models strongly affects peasant behaviour in their synthetic chemical usage. Their behaviour is their strategy to survive in specific dilemmas and reflects their niche. Pesticide poisonings are the product of the risks created by the current agri-food supply system. More attention should be paid to the agri-food system itself and its governance. The alternative supply approaches might provide a way out of the dilemmas for Chinese peasants and agri-food safety.