The governance of the STI policy covers a wide range of practices and activities related to complex interactions among different actors in order to converge the conflicting interests in the policy process. Since the concept of innovation is horizontal, interorganizational, and inclusive, and also is known as a result of complex interactions and the evolution of actors, their institutions and their relations, and because of the extension of its scope from science and technology to other policy areas such as education, health, Agriculture and industry, the study of governance in STI policy seems essential. In this article, Iranian innovation policy making governance during 1990 – 2019 is studied by historical data mapping method. Generally, four main stages for STI policy making can be defined as follows: First stage includes initial attention to horizontal and political coordination and higher education quantitative development according to human resource based approach to scientific progress. In the second stage, focusing on policy coherence in science, technology, innovation and institutionalization for them. The third stage includes focusing on integrated planning and monitoring in addition to innovation horizontal policies. Finally, in the fourth stage, understanding the importance of policy intelligence & learning and focusing on deployment of technology in different parts of Iran economy. Totally, during all these four stages, network governance impact on STI policies from higher education to other parts of Iran economy is significantly emphasized. However, there are some challenges in this category such as overlap between different institutions and policies, inadequate policy intelligence and policy learning and non-optimal evolution of governance. In particular, the promotion of coordination between the actors in this area and other economic and political actors in the country and the creation of coherence and integration among these policies, especially between science policies and innovation policies in order to create economic value are the most important issues that this approach can address them.