Innovation system is one of the most important segments of planning in every country which is needed for economic and social prosperity, security and welfare. But the lack of achievement to scientific purposes in Iran indicates that there are many challenges toward innovation system and its progress. In the other word, it is necessary for improving national innovation system to be affected by consistent and clear policies. It means that a kind of policies is needed which can define the contribution of each players in the innovation system and the rate of their participation. Achieving to this goal, makes us to use a scale for measuring the policies and let us to evaluate and identify the pros and cones. Also, this approach toward the innovation system makes it better than the past and helps us to create more functional and strategic policies in the future. For this goal, we study a wide theoretic framework and 16 previous studies to suppose a functional scale consist of five levels named: Management and policy making, producing and accumulating the knowledge, distributing knowledge, applying knowledge and infrastructure. The results show that there are 159 weaknesses and shortcomings in innovation system according to the opinion of experts. In addition we supposed 43 indicators related to five levels scale for making functional policies of innovation in the future.