The higher education system is recognized as one of the most important factors of any society for development and progress. The main purpose of this study was to design and validate a model for social-cultural structure of universities. The research method was applied and developmental in terms of purpose and explanatory sequential mixed and modeling type in terms of data collection method. The initial theoretical framework was developed and validated in three stages using multiple data matching methods. In first stage, in order to identify the components of the social and cultural structure of universities, 46 study units were selected and studied. In the second stage, the interview was conducted in a semi-structured and purposeful manner with 16 experts and informants in this field. In the third stage, using stratified sampling method, 378 educational and non-educational staff were selected from 8 different universities. In the first stage, categorization document content analysis method was used for data analysis. In the second stage, categorical content analysis method was applied and in the third stage, Partial Least Squares, PLS adopted to validate the model through SMART PLS 3 software. The research results showed that the social and cultural structure of universities includes 12 main components including trust, shared norms and values, mutual understanding, group dynamics and participatory actions, information channels and network communication, risk-taking and innovation, leadership and management, structure, evaluation, honor and dignity, mission, independence and freedom. Therefore, the identified components of this research can be a good basis for evaluating, understanding and improving the social and cultural structure of universities by higher education policy maker institutions in Iran.