The synergies for the Iranian regional and national innovation systems among the geographical, technological and organizational distributions of firms were measured. Among the data of 87934 active industrial firms (December 2015), merely 46150 firms could be classified using NACE codes into high-tech, medium-tech and knowledge intensive sectors which in turn geographically divided into five regions. Accordingly, both the T0 and ΔTGTO of Iran at the national level had negative signs (-480.6 and -5.14 mbits, respectively), however all the ΔTGTOs in each separate region was highly positive denoting that national agglomeration significantly adds to the synergy in the system and a highly integrated national innovation system was proposed in Iran. Regions 1 (including Tehran as the capital) as well as region 4 (including Khuzestan which contains enormous oil and gas resources and industries) caused less disturbance to the national synergy compared with the other three regions (ΔTGTOs= +18.1 and +22.2 mbits, respectively). The decomposition of sectorial technologies showed that in contrast to many other countries, especially for west European countries, high-tech manufacturing and knowledge intensive services were the main drives of knowledge-based configuration in the regional economy of Iran, while medium-tech manufacturing tend to uncouple the economy from the regional configuration