At present, the question of the key directions of transformation of the university model is quite acute. First, it helps to rethink the relationship between all participants in the innovation process in the format of a civilizational transition to new forms of cooperation and partnership. Secondly, it complements the existing models with an emphasis on the quality of life, happiness, and changes in the urban and regional environment. Thirdly, it improves the educational and scientific processes through the introduction of up-to-date pedagogy, educational technologies, as well as technologies of scientific research and the activation of innovative activities. The objective necessity of studying this problem in theoretical and methodological aspects confirms the relevance of the research topic of the authors’ team. The purpose of the study is to develop a methodological approach to conducting organizational diagnostics of the university as a driver of innovative development of the region for planning and implementing its transformations. Using general scientific and special methods of scientific research, the authors have studied the main approaches and models of university transformation in Russian and foreign practice. The main emphasis is placed on the possibility of transforming the university for the purpose of innovative development of the region, taking into account the concept of “smart specialization”. It is established that according to the model of the “four-link spiral of innovation”, a modern university is an active stakeholder in the innovation process. In this regard, the role of higher educational institutions in the formation of regional innovative development programs based on the principles of “smart specialization” is determined. The functions of universities as groups of “Science and Education” stakeholders at each stage of this strategic process are highlighted, which emphasizes the scientific novelty of the research. To plan and implement measures for the transformation of the university model as an element of the regional innovation system, the authors propose a method for organizational diagnostics and structuring problems as an analytical step for future transformations of the university. The directions of further research of the authors will be aimed at studying the problems of interregional cooperation of universities as stakeholders of the innovation process.