This article describes and analyses the renovation of the mechanism on Japanese science policies' formation and it's practice. Firstly, it explains the reorganizing of the institutional system. The early Japanese Science and Technology Meeting was changed, and the new synthetic Science and Technology Meeting was established, which is directly in charge of the Cabinet. Secondly, the paper deals with the initialization of the second step of the fundamental scientific plan. Japan has made sure four key research fields and series of guiding to develop science and technology. Finally, the paper analyzes and indicates the new trend of the institutional system change and the public scientific policies' development resulted from the renovation of the scientific knowledge's production mode.