In recent years, agriculture products have contributed to 28.75% of Thailand’s GDP. China, Vietnam, Myanmar, Cambodia, Laos and Vietnam are the main markets for agricultural products. The annual export volume exceeds 119,222 million THB. The majority of them are shipped over Thailand’s land borders to its neighbors. Small and medium-sized farmers make up more than 85% of those who produce agricultural items. Numerous scholars have studied the transportation methods used by the Greater Mekong Subregion (GMS) nations along the economic corridor, but the majority of them have concentrated on import–export operations involving sizable firms, which are not applicable to the transportation of agricultural products, particularly when attention is paid to small and medium-sized farmers. In this study, mixed-integer programming (MIP) is presented to design an agricultural product logistics network. In order to prolong the lifespan of the container used, the MIP’s primary goal is to maximize the total chain profit while maintaining the lowest container usage possible. The approach was developed to increase small and medium-sized farmers’ ability to compete. Small and medium-sized farmers bring their products to an agricultural product collecting center, also known as a container loading facility. After that, skilled logistics companies distribute the goods. In order to convey the goods to the final clients in neighboring nations, the proper locations of the containing loading centers, the correct transportation option and the borders must be decided. The issue was identified as multi-echelon location–allocation sizing (MELLS), an NP-hard problem that cannot be handled in an efficient manner. To solve a real-world problem, however, efficient techniques must be supplied. AMIS, an artificial multiple intelligence system, was created to address the suggested issue. AMIS was developed with the goal of leveraging a variety of methods for local search and development. There are several well-known heuristics techniques employed in the literature, including the genetic algorithm (GA) and the differential evolution algorithm (DE). With respect to the improved solutions obtained, the computational results show that AMIS exceeds the present heuristics, outperforming DE and GA by 9.34% and 10.95%, respectively. Additionally, the system’s farmers made a total of 15,236,832 THB in profit, with an average profit per container of 317,434 THB and an average profit per farmer of 92,344.44 THB per crop. The container loading center uses 48 containers, with a 5.33 container average per container loading center (CLC). The farmers’ annual revenues were previously less than 88,402 THB per family per year, so we can predict that the new network may increase customers’ annual income by 4.459% for each crop.