This study aims to provide comprehensive guidelines for effective and sustainable system‐wide transformation in innovation policies by considering emerging challenges and trends. For effective survival and growth in advanced technological environment and fast‐changing market environment, changes and innovation are integral for organizational structure. Our suggested framework explores the key challenges facing to contemporary innovation systems; these challenges are experimentation, demand assessment, directionality, coordination and learning. This also study considers the generic features of innovation systems like actor's capabilities and interest, network and proper institutional set‐up. These three generic features can translate experimentation, demand articulation, directionality, coordination and learning to quantifiable and make them policy analysis oriented. Our proposed framework advocates that organization innovation policy should consider actor, network and institution‐focused models. Otherwise, the transformational change will be overly abstract, a non‐actionable policy agenda, and unable to provide a complete picture of challenges at the operational level.