This study clarifies the relationship between spatial proximity and innovation networks by analyzing and comparing Korean and Japanese innovation systems. These systems have their similar backgrounds, but different innovation policies. The structural features of these innovation networks include hubs, sub-groups, and islands with pipeline linkages. The innovation network is formed by mixing of organizational proximity and geographical proximity within urban systems. Therefore, innovation policy should consider these network structure and urban system patterns, with flexible network governance. In addition, the innovation network can be successfully fostered through promotion policies within a single region rather than as distributions across regions.