Despite the growing importance of developing countries to the global economy and their increasing role in innovation, limited academic attention has been given to the national innovation systems (NIS) of these countries. Given that they commonly suffer a lack of resources, efficiency in the operation of innovation seems crucial. This study aims to assess the innovation efficiency of developing countries. Breaking down the NIS into two stages, knowledge production and application process, we additionally introduce the knowledge absorption perspective in the latter stage as the consideration for the context of developing countries. Based on the results of the efficiency assessment, clustering analysis is implemented to identify several typologies of the operation of NIS in developing countries and to provide implications for each case. This study will constitute a meaningful attempt to provide a general understanding of innovation status and operations in developing countries, thereby suggesting policy directions for several cases.