Despite Iran’s significant capacity in strategic agricultural products, its food security faces heterogeneous challenges across farm, market, and policy levels, exacerbating food distribution imbalances, severe price fluctuations, and limited natural resources. The absence of an integrated framework that can simultaneously combine bio-economic-policy factors into actionable scenarios toward 2036 (1415 in the Iranian calendar) is evident. This gap underscores the necessity of a structured method linking micro-level data with macro-level decision-making. The present study aims to design and validate a morphological-scenario model to analyze key factors influencing national food security with a focus on strategic agricultural products. The research employed a mixed-method approach with an exploratory sequential strategy; in the qualitative phase, six primary drivers were identified through document review, while in the quantitative phase, 6,400 possible combinations were evaluated using Morphol software and data from 30 experts, leading to the selection of two optimal scenarios. Findings indicate that the ideal scenario (probability 0.78) simultaneously requires “over 30% reduction in production costs,” “full infrastructure improvement,” and “extensive technological innovation,” yielding the highest positive impact on food security indicators. The alternative scenario (probability 0.62) offers moderate performance with intermediate levels of the same variables. The greatest resistance to change (inertia) is linked to “weak policies” and “low support for local markets.” The results align with international studies and, for the first time in Iran, bridge the gap between micro-level data and macro policies through a morphological approach; the proposed model is applicable to other developing countries facing water and soil resource constraints.