The present study was conducted with the aim of presenting a model of good governance in higher education based on the university ecosystem. For this purpose, a mixed research approach was used. In the qualitative part, the main components of the model were identified through semi-structured interviews, and in the quantitative stage, the validity of the proposed model was tested using data collected through a questionnaire. The statistical population of the qualitative part of this study consisted of specialists, experts, and managers related to Iranian higher education policy-making, who were selected using the snowball sampling method. This process continued until theoretical saturation was reached. In the quantitative part, the statistical population included faculty members of Islamic Azad Universities in Tehran, who were selected through stratified random sampling; at this stage, 183 people participated in completing the questionnaires. The qualitative data obtained from the interviews were analyzed using the phenomenological method and coding technique. The results of the qualitative analysis identified the components of policy-making and governance, educational institutions (universities), innovation and technology, research and science production, human capital, industry-society relations, financial resources and support, international interactions, and digital infrastructure and information technology as the main elements of good governance based on the university ecosystem in Iranian higher education. Also, in the quantitative part, data analysis was conducted through structural equation modeling and confirmatory factor analysis using PLS software. The results of the factor analysis showed that, respectively, policy-making and governance, industry-society relations, financial resources and support, international interactions, and human capital have the highest factor loading in influencing the efficiency of the good governance system in Iranian higher education.