Purpose: Scientific-applied education as higher education needs coherent and structured planning. So, this study was conducted with the aim of explaining the challenges and obstacles of the application of land use planning in the development of scientific-applied higher education. Methodology: The present study was of applied in terms of purpose and qualitative in terms of implementation method. The research community of land development planning documents in 2001-2020 and experts, including faculty members, managers and experts of scientific-applied higher educations in 2021, based on the principle of theoretical saturation, 35 cases of land development planning documents and 23 experts with targeted sampling method were selected as samples. The research tools were note-taking of documents and semi-structured interviews with experts, whose validity was confirmed by the opinion of experts along with triangulation method, and the reliability was obtained by the method of agreement coefficient between multiple coders of 0.85. Finally, the data were analyzed by thematic analysis method in Maxquda-12 software. Findings: The findings showed that 50 basic themes, 8 organizing themes and 5 comprehensive themes were identified for the challenges and obstacles of land use planning in the development of scientific-applied higher education; So that comprehensive themes includhng assessment of skill training needs (with two themes organizing labor market information bank, products and products with local and regional participation and curriculum design and revision), ecosystem, ecology and regional population (with two themes organizing economic activities and commercializing scientific-applied and training, empowering and scientific-applied professional qualifications), organizing and polarizing optimally in terms of space and time (with an organizing theme of the geographical arrangement of polarization and mission-oriented scientific-applied education centers), provincial and regional governance (with an organizing theme of local partnership management) and scientific-applied higher education preparation (with two themes organizing the training, superior laws and documents, challenges and obstacles in the use and application of the preparation of the land). Conclusion: According to the findings of this study, it is possible to use the basic, organizing and comprehensive themes identified to reduce the challenges and obstacles in the application of land use planning in the development of scientific-applied higher education.