Despite the quantitative expansion of higher education and the growth of scholarly production in the humanities in recent decades, these developments have not proportionately contributed to improving governance quality, public policymaking, and the resolution of social problems in the Islamic Republic of Iran. This situation indicates that the main challenge is not the lack of knowledge production, but rather the institutional disconnection among science, government, and society, which has limited the transformation of knowledge into policy, institutions, and social action. This study aims to explain the dimensions of this institutional disjunction and present an indigenous framework for reconstructing the relationship among science, government, and society. The research is qualitative in nature and employs documentary and conceptual analysis methods. Data were collected through the study of academic books, scientific articles, policy documents, and relevant sources in the fields of knowledge governance and science policy, and were analyzed through theoretical inference. The findings reveal three major institutional gaps: within scientific institutions, including weak problem orientation and limited engagement with policymaking; within governmental institutions, including inadequate mechanisms for evidence-based policymaking and knowledge translation; and within society, including the decline of the social authority of knowledge and weak feedback mechanisms. Based on these findings, the study proposes a framework consisting of five components: professional wisdom, affirmative problematization, shared epistemic identity, knowledge translation, and redefinition of the functions of scientific institutions. This framework can contribute to strengthening knowledge-based policymaking and enhancing the role of humanities in governance.