This study discusses the structure of Turkish National Innovation System (NIS) and challenges faced in the last decade in the context of the digital transformation. As a developing country and a member of G-20, how these challenges of Turkish NIS are mitigated and further be dealt with. It comprises lessons and provides cases for various similar NISs. In order to evaluate and provide policy recommendations for accelerating the transformation of Turkish economy, it benefits from systems approach as a basic academic framework. It is found that Turkey faces four key structural challenges calling for urgent response for their targets of 2023 (hundredth year of the Republic), namely productivity, growth, employment and investment. Implementing a relatively simple rule compatible with the peculiarities of the system and focusing on the diversity of policy mix, the study proposes ways to mitigate these structural challenges towards digital transformation.