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Amidst the rapid expansion of farmer cooperatives in China, effectively leveraging these organisations to encourage members to reduce chemical pesticide use holds significant implications for ensuring food safety and advancing high-quality agricultural development. Existing research has predominantly focused on whether farmers joining farmer cooperatives influence their green production behaviour, while generally overlooking the pronounced heterogeneity among farmer cooperative members in China. Ordinary members’ choice of the farmer cooperatives’ transaction model essentially constitutes a proactive embedding within different institutional arrangements. The series of contractual designs, oversight mechanisms, and incentive structures underpinning the farmer cooperatives’ transaction model influences members’ green production practices. Therefore, based on survey data from 608 farmer cooperative members in Sichuan Province, this paper employs an endogenous switching regression model to construct a counterfactual framework. Addressing endogeneity issues reveals that members’ selection of the farmer cooperatives’ transaction model favours improved chemical pesticide reduction behaviour. The transmission mechanism shows that the improvement in members’ chemical pesticide reduction behaviour, driven by the farmer cooperatives’ transaction model, stems from, in order of contribution, surplus distribution incentives, product delivery standards, production factor input constraints, and production service incentives. Heterogeneity analysis further indicates that the transaction model of farmer cooperatives with companies, fruit merchants, and e-commerce platforms enhances members’ chemical pesticide reduction behaviour by 57.6%, 43.4%, and 44.3%, respectively. To strengthen the role of farmer cooperatives in promoting agricultural green transformation and chemical pesticide reduction, this paper proposes four policy recommendations. First, refine internal governance within farmer cooperatives to strengthen institutional designs that balance incentives and constraints. Second, expand stable partnerships between farmer cooperatives and companies to establish robust order systems and deep cooperation models centred on ‘premium prices for premium quality. Third, enhance technical training and unified agricultural input services to reduce transition costs for members. Fourth, leverage demonstration effects within villages to create a collective atmosphere for green production, using ‘group effects’ to drive a holistic transformation among members.