The empirical evidence shows that the Information Technology (IT) has a critical role in the economic growth of developed countries. Thus, the developing countries interested in economic development should be aware of the ways of employing technological innovations for achieving this goal. Innovation System approach is a pervasive method to analyze the technological innovations. However, this approach has not yet reached to the thoroughly conceptual integrity. In this paper, using the concept from Enterprise Architecture (EA) discipline as well as Innovation System theory, we have introduced a new concept called IT Innovation System Architecture and an accompanied framework. This framework is derived from Zachman framework in the EA field. Also, an institutional analysis of IT diffusion in Iran has been done. The research method employed in this paper is a survey on 42 institutional entities. Results represent very institutional shortcomings in IT diffusion in Iran. Finally, as a policy implications, it has been proposed that this framework could be used for analysis of other technologies in the national level and even national innovation system as a whole.