Inconsistency quality and availability of cocoa beans become a serious problem for cocoa agro-industry. In general, we can not trace whose cacao beans are processed in the industry. This is due to the lack of integrated supply chain consisting of farmer, collector, trader, exporter and industry. This study aimed to produce a design of competitive cocoa agro-industry supply chain system with dynamic system approach. Integrated partnership between Sidodadi farmer’s group in Putat village, Patuk subdistrict, Gunung Kidul district with TTP Nglanggeran, Cokelat nDalem and local collector give a competitive value for cocoa agro-industry supply chain. Through this, fermented beans directly distributed to industry and processed. Cocoa supply in scenario increase 2.61% from existing, decreasing the balance of cocoa beans supply demand up to 0.7%, raising the first level of cocoa beans quality up by 2022, and lifting the accumulation of Farmers group’s profit up to 29.31%. The design of this system is expected to inform cacao stakeholders about the importance of partnerships to improve cocoa agro-industry competitiveness.