This study is an exploratory investigation on how national R&D investments decisions are made in Korea. For developing system dynamic model, we are interested in locating three structural dilemma, occurring with the Korean NIS. In so doing, we intend to devise the ways of ameliorating problems within the NIS investment decision-making process by providing policy implications. We identify delays and side effects during transition periods between different stages of technology innovation by perceiving the switching pattern dynamically, in which form of technologies shifts from one to another stage like paradigm shift, when the R&D investment reaches a certain stock. It is also suggested that the development of strategies is necessary in order to enhance efficiency of technological development process.