Background and Aim: As the first and most important educational institution of the country, the school plays a decisive role in teaching ecological literacy along with other organizations and educational tools. The purpose of this research was to design an interpretative structural model of the challenges of developing ecological literacy in secondary schools. Methods: The current research is of mixed type (qualitative and quantitative). In the first phase, a qualitative research method was conducted using thematic analysis, and in the second phase, a quantitative method was conducted based on interpretive structural modeling. The statistical community in both qualitative and quantitative sections, due to the expert-centeredness of the interpretive structural modeling approach, formed experts, which included school principals, teachers, environmental education experts, environmental education professors, and environmental elites. They were selected purposefully and until theoretical saturation was reached (22 people). Sampling method in the quantitative part, due to the expert-oriented approach of interpretive structural modeling, the experts were in the qualitative part (N=20). The measurement tool in the qualitative part was a semi-structured interview and in the quantitative part, a questionnaire. Validity and reliability of the data were confirmed. Two methods of thematic analysis (Max QDI software) and Interpretive Structural Modeling (ISM) (Excel software) were used to analyze the data. Results: 6 main themes of ecological literacy development challenges in secondary schools have been identified, which include human, infrastructure, economic, attitudinal, curriculum and political challenges. Conclusion: Human challenge and curriculum are in the independent cluster, that is, it has a great influence on other factors and other factors have little influence on it; The themes of infrastructure and curriculum are placed in the dependent cluster, that is, they are affected by other factors and have little effect on other factors; Economic and attitudinal themes are placed in the linked cluster, that is, they both influence other factors and are influenced by other factors.