Institution is a controversial concept in the economic literature and after more than one century, there is still no unanimous definition for it. However, many economists have studied its role and importance in many contexts including National Innovation System (NIS). In NIS context, some researchers argued that institutions are X-efficient and X-effective but they didn't open up that much about how to measure them. In this study, using the elements of performance including efficiency, effectiveness and changeability, a typology of institutions in NIS is suggested. Since institutions are investigated in the context of a system, inputs and outputs of each institution in its relationship with other institutions are selected as the base for measuring performance elements. In order to use the suggested typology, performance elements of 8 institutions in Iran's national innovation system are measured and 8 strategies – including growth, exhaustion, displacement, layering, drift, operational efficiency, conversion and status quo-are proposed to improve the performance of each type of institutions. The results showed that accurate extraction of inputs and outputs of each institution in its relation with its next institutions in NIS and measuring its performance elements would help policy makers to identify the gaps in relational performance of institutions in NIS. Also, considering the speed of change for each institution could help policy makers to select the right time horizon for making changes.