Role of digital infrastructures to improve data exchange on trade lanes becomes more critical as complex border procedures contribute to inefficiency of the international supply chain. However, digital infrastructures innovation in international trade (DTI) has not reached the implementation phase. We are interested to analyse digital trade infrastructures innovation process based on its innovation system. The dynamic of innovation system influences the speed of innovation process. We argue that the blockages and unblocking strategy of DTI innovation process can be clearly identified if the innovation system is examined by looking at two levels of analysis, which are structural, related to changes in system’s structure (e.g., actors, networks, governance) and functional, related to the ability of such system to perform certain functions towards achieving its objectives. To the knowledge of the author, there is no theoretical lens which discusses activities and events happened in DTI innovation system to a detailed breakdown of its structural or functional changes. Mainly the existing studies only focus on using the innovation system analysis as the analytical tool for directing innovation policy and neglect the collective action process that is very relevant with characteristics of DI development. Therefore, the research objective is to create and apply a conceptual framework, to identify the unblocking strategy for digital trade infrastructures innovation process by looking at structural and functional analysis of the innovation system. We develop conceptual framework namely Structural-Functional Analysis Framework, based on the desk research. We evaluate the framework through a longitudinal IT innovation case study on EU funded project. Documents analysis and interviews are employed as data collection methods. From the framework evaluation, this study reports that the combination of analyses concerning structural changes and functional performance of an innovation system is capable to provide richer explanation on issues that limit an innovation system to further develop the DI innovation, a strategy that can be done to mobilise the innovation process, and the DI innovation process itself.