The aim of this study is to diagnose the weaknesses of the science and technology priorities section in Iran’s National Comprehensive Scientific Map and propose strategies for its structural and procedural improvement. This research employed a qualitative approach using thematic content analysis. Data were collected through semi-structured interviews with 18 experts, policymakers, and senior managers in the science and technology sector. Participants were selected via purposive sampling until theoretical saturation was achieved. The data were analyzed through open and axial coding, resulting in the identification of major and subcategories. The results indicated six main categories of challenges in the current priorities framework: structural deficiencies, weaknesses in the prioritization process, misalignment with national needs, implementation obstacles, institutional governance issues, and lack of updating and foresight mechanisms. Each category contained components such as centralization, lack of stakeholder involvement, missing budgetary frameworks, and insufficient attention to emerging technologies. Based on the findings, a comprehensive redesign of the science and technology priority-setting process is necessary. It is recommended that mechanisms for institutional participation, data-driven methods, and continuous evaluation systems be developed to enhance the effectiveness of science and technology policy in the country.