The aim of this study is to discover how inter-subjectivity is formed among various organizations in horizontal relationships as a basis of sustainable collaborative innovation. Since each organization in a horizontal relationship is independent, generating a sustainable project among multiple organizations is different from one within an established organization or one among organizations in vertical relationships. Forming inter-subjectivity among organizations is required as the founding phase of collaborative projects. The authors have empirically approached this problem and introduced the research methodology of dynamics, referring to knowledge creation theory. The results of our study demonstrate that it is essential to form inter-subjectivity among collaborators, which could be the base for dynamic innovation shared by stakeholders. Further, the outcome of this study will likely contribute to the development of the design methodology for innovation ecosystems among organizations in horizontal relationships, as well as to the substantial expansion of the scope of knowledge management theory.