The purpose of this study was to identify and explain the challenges and deficiencies of skills training at the National Skills University of Tehran based on the three-branch model encompassing content, structural, and environmental dimensions. This applied qualitative study was conducted among managers, faculty administrators, educational experts, and specialists affiliated with the National Skills University of Tehran. Participants were selected through purposive sampling, and semi-structured interviews were carried out until theoretical saturation was achieved with 18 interviewees. Data were collected through document analysis and in-depth interviews and subsequently analyzed using qualitative procedures. Face and content validity were confirmed through expert review, while reliability was assessed using the test–retest method, yielding a reliability coefficient of 0.70. The findings revealed that skills training at the National Skills University suffers from substantial challenges across all three dimensions of the three-branch model. In the content dimension, 15 deficiencies were identified within educational needs assessment, curriculum planning and design, instructional implementation, and educational evaluation. Key issues included inadequate alignment with labor market demands, outdated educational content, obsolete workshop and laboratory equipment, and the absence of competency-based assessment systems. In the structural dimension, seven deficiencies were identified, primarily related to the lack of a structured management system for skills education and inadequate mechanisms for private-sector engagement. In the environmental dimension, six challenges emerged under socio-cultural and economic barriers, including credentialism, negative societal attitudes toward vocational education, insufficient financial support, and economic recession affecting industry and employment opportunities. The study demonstrates that improving the effectiveness of skills training requires simultaneous reforms in content, structure, and environmental conditions. Aligning educational programs with industry needs, continuously updating curricula and facilities, decentralizing management structures, strengthening partnerships with the private sector, and expanding economic and social support for graduates can significantly enhance the quality, relevance, and sustainability of skills-based higher education.