It is general that mostly congested sections of national backbone networks have been improved based on the national network expansion plan. However, in case of intermodal terminals which are origins of logistics, it is still so congested that travel time between origin and destination is long. Therefore, intermodal transportation systems plan of major intermodal terminals for the intermodal connector networks between intermodal terminal and national backbone network or intermodal terminal was established. With the limitation of priority methodology applying to intermodal connector facility under existing methodology, this study suggests an improved priority methodology. This study includes characteristics of terminal on the hierarchical structure and assessment list, but it does not concentrate on the specific terminal type through survey. To avoid a certain concentration, budget constraint for each terminal type was considered ahead of priority. Finally priority methodology was developed with two-step assessment under consideration that specific terminal is not involved in intermodal connector facility project. As a result of calculating weights by survey, effects such as d/c and accessibility fluctuations index through project implementation gain high weight, and degree of region underdevelopment gets next. Although the methodology in this study could not yields the priority by assessment list, it will be useful for setting the direction on policy related to intermodal connector facility projects.