BACKGROUND: The issue of academic autonomy along with the reduced authority of the government for handling the service-providing section is considered an urgent demand for most of the organizations including hospitals.METHODS: The method of research was a combination of quantitative and qualitative methods from sequential exploratory studies type. In qualitative part, descriptive-phenomenological method using seven-step Colaizzi method and in quantitative part, survey method was used. Statistical population of research of the first part included key experts of the academic autonomy field who were selected purposefully and based on the criterion. With 8 persons, data were saturated. Data collection tool of this part was semi-structured and deep interview. Validation of data was performed by outsider auditors as well as through returning to the interviewees. In quantitative part, a 60-question questionnaire made by the authors was used for data collection which was distributed among officials including hospital managers and key stakeholders of the academic autonomy process in a heart hospital who were 98 persons. Superficial and content validity of the questionnaire was estimated as much as 0.70 for all items. Modeling analysis in inferential level was done through Akaike scale regression.RESULTS: Academic autonomy is in three dimensions: economic, scientific, and organizational and inter-organizational, intra-organizational, and extra-organizational factors contribute to it from which scientific autonomy is more important compared to other factors. Moreover, intra-organizational factors have more contribution to the academic autonomy of these centers.CONCLUSION: The results of this study will be a good guide for academic autonomy of medical centers. In order to achieve academic autonomy, it is more important to pay attention to factors such as autonomy culture capacity, independent signing treaties and international documents, and science-centered society.