Abstract: From the perspective of institution and legitimacy, exploring the dynamic interaction of the medium and micro levels, and explores how the institutional environment promotes and constrains the interaction of innovation actors which eventually builds the consensus space of triple helix system. Taking the construction process of a big science project in China as the research object, using a mixed qualitative research method of case study and grounded theory to analyze data. Finding that institution, as the environmental factor of innovation Triple Helix system, is an important dynamic factor in the construction of consensus space; individuals’ legitimacy propriety and the organizational legitimacy validity of institutions form legitimacy pressure/support, leading to legitimacy spillover/loss, which influence the construction of the consensus space by extending the consensus or dissent space boundary.