In the logistics operation of fruits and vegetables represented by the apple, pear, persimmon and mandarin, the difficulties with intermodal transportation between producers and consumers, which are driven by the rising packaging costs due to the use of one-time corrugated cardboard packaging materials and the reality of loading and unloading by the loading and unloading labor at public wholesale markets, have increased logistics costs. This study proposed an intermodal transportation plan with the use of packing containers of reusable materials to replace one-time corrugated cardboard packaging materials as a measure to deal with the difficulties. The study also developed a logistics rationalization model for intermodal transportation of fruits and vegetables by examining the stages of transportation among producers, public wholesale markets, and retail markets, the circulation routes of fruits and vegetables, and analyzing the costs through the transportation process from producers to retailers as well as the packaging costs and loading and unloading costs. Furthermore, the study demonstrated that intermodal transportation and logistics costs could be reduced by using reusable packaging containers that could be loaded by the pallet unit from producers in the producing areas to public wholesale and retail markets through numerical analysis of packaging costs, transportation costs, and loading and unloading costs.