Abstract: Institutional and structural problems are the key issues in the construction of the system of regional civil-military integration innovation. A interpretive framework of boundary building and boundary change in regional civil-military integration was formulated by introducing the concept of boundary permeability and employing a grounded theory, with an industrial functional zone in Chengdemian region as an example. Research finds that, since the whole innovation system is embedded in complex institutional environments, different actors, following various institutional logics, build different kinds of boundaries, including boundary strengthening, boundary crossing, and boundary blurring, and form three modes of alliances. What is more, the different types of boundary permeability and alliances impact the efficiency and effect of the process of civil-military integration.