This article reviews transition of research funding system and the impacts for national innovation system. The origin of innovation depends on science and technology. The leaders of science and technology are scientists. If scientists take any impacts, it also affects innovation system. It is research funding that train scientists and support their research. If scientists do not take research funding, they will not be able to proceed their research. It depends on funding whether they can research or not. Transition of research funding system affect behavior of scientists and their outcomes. This article firstly reviews background of transition of research funding system. Also, we show some representative research funding systems and examine how research outcomes are produced under the systems recently.