Systemically, agricultural research considers as main component of agricultural knowledge and information system (AKIS) and plays importance roles in process of sustainable agricultural development in field of developing knowledge and technology. Considering expected outcomes and impacts, influencing factors, current challenges, and emerging paradigm of research and development (R&D), Iranian agricultural research system needs institutional supporting based on designing and implementing appropriate strengthening mechanisms. Regarding to this comment, this research was done with the aim to identify challenges and explain strengthening mechanisms of agricultural research system in Iran. A survey research and qualitative expert interviewing methodology were applied, a sample consisted of 29 agricultural researchers and agricultural faculty members was selected. After designing interview protocol and gathering data by interviewing, coding process used in order to analyze the interviews. Findings presented in a structural format, including open, axial, selective and subjective categorized codes. Based on integrated interpretation of subjective categorized codes, some conceptual propositions were formulated in field of challenges and systematizing of agricultural research in Iran. Systemic and process-derived conceptualization procedures were used in order to process the findings. As a result, a representative model of agricultural research system was outlined. This model explains different structural and functional aspects of agricultural research system and seems as pattern of emerging paradigm of agricultural research. Finally, using an interpretation-explanation approach, a set of appropriate mechanisms of systematizing and strengthening of agricultural research in Iran were recommended.