The main purpose of this article is to suggest policy implications for building innovative cluster in Korea by investigating the operating system and role of the Kanagawa Science Park (KSP) located in Kanagawa prefecture, Japan as a central network agent. The KSP established mainly by private and government partnership has played a critical role for building innovative clusters as a way in which increase national competitiveness. But they also provide variety of real service from R&D to commercialization for local firms by facilitating and coordinating networks among regional economic actors such as firms, universities and public research institutes. The regional policy as a way in which increase national competitiveness in Korea is also the establishment of innovative clusters based on regional and industrial characteristics. However, the main problem with building the innovative cluster is the reduction of policy effectiveness due to duplicated supporting and coordinating institutes and institutions established by the each central administration and local governments, aimed at facilitating networks among regional economic actors. In this context, the article suggests that there is a need to build a regional central network agent by designing an organic operating system for the effective management of each network agent in accordance with the process from R&D to commercialization, i.e. an encompassed supporting system, on the basis of benchmarking the KSP operating system in Japan.