Thailand is the world’s leading agricultural products exporter. The transportation of agricultural products in Thailand relies mainly on roads because of its extensive network and convenience. However, with the limited capacity, traffic congestion, air pollution, and high fuel prices, this transportation mode becomes less effective. The government, then, attempts to develop and promote multimodal transportation, especially rail and water modes, to reduce the logistics costs and increase the transportation network efficiency. This study extracts five key factors influencing multimodal transportation efficiency of agricultural products in Thailand, namely Multimodal Transportation Infrastructure, Operation, Multimodal Service Provider, Market, and Road Constraints factors, as well as examines their interrelationships using the structural equation modeling method. The results show significant direct and indirect relationships among the five key multimodal transportation efficiency factors. It is found that with better multimodal transportation-related operations, multimodal transportation market is improved through less use of road transportation and more multimodal service providers in the market. Moreover, policymakers should focus on improving multimodal transportation-related infrastructures, such as container yards, access roads to train station and port, and transshipment equipment, in order to increase multimodal transportation efficiency and encourage the use of multimodal transportation. Engineering managers can use the study results in decision-making of transportation mode selection. Policymakers in government sector may apply the study results to establish effective policies to achieve a sustainable transportation system, which, in turn, gives rises to national industrial competitiveness on a global scale.