This study investigates the complex relationships among factors affecting post-harvest losses in agri-food supply chains, with a particular focus on the role of logistics efficiency management. Using data collected from agricultural supply chain stakeholders, the study employs structural equation modeling and fuzzy-set qualitative comparative analysis (fsQCA) to examine both direct relationships and configurational pathways leading to post-harvest losses. The results reveal that logistics efficiency management significantly reduces post-harvest losses both directly (β = -0.423) and indirectly through enhanced supply chain coordination. Information management efficiency demonstrates the strongest influence on logistics efficiency management, while infrastructure quality, technological adoption, and farmer knowledge contribute to reducing post-harvest losses with relatively small effect sizes. The fsQCA results identify multiple sufficient configurations for both high and low post-harvest losses, with the presence of logistics efficiency management and supply chain coordination consistently associated with lower losses. Climate and environmental conditions positively moderate the relationship between logistics efficiency management and post-harvest losses, while government policies and regulations show a negative moderating effect. This study contributes to the literature by providing empirical evidence for the complex interrelationships among factors affecting post-harvest losses, demonstrating the critical role of logistics efficiency management, and offering practical insights for policymakers and practitioners through configurational analysis.