The article is oriented towards a certain problem. It analyses modern practice of university organizational development, problems and challenges of the process and gives recommendation on improving university activities in this sphere. Traditional formats of university education organization need to be developed further, new models and structures must be created. Lately the search for the most effective solution for organizing universities and their networks was the priority topic for educational policy in many countries. Russian Ministry of Education strategy till 2020 suggests alterations in typology and structure of university network by means of decreasing the number of universities and their branches. At the same time analysis of this strategy implementation reveals several challenges that call for making changes in the policy itself. The article analyses the process of appearance and functioning off university branches network, its role in solving the problem of education accessibility in the crisis context; provides foundations for changing approaches to university structures decrease in the modern context; suggests new ways and methods of remote branches functioning including their status as university network structure units. These decisions would facilitate formation of a more balanced structural changes policy and preservation of regional remote braches network as an important aspect of education accessibility and enriching social environment of smaller and medium towns in the country. The article also looks into the process of university mergers and inclusions, conducting comparative analysis of practice in this field in retrospective and inter-country aspect. Taking into the consideration a large number of inclusions to form pillar universities the authors analyze key problems of this organization change and suggest solutions decreasing conflicts in the merger process and improving its efficacy. An important aspect of university organizational development analyzed in the article is a convergent structure, built on cooperation of the participants. The article analyses peculiar features of such structures, their role in in university strategies implementation, limitations and problems in their activities and provides recommendations on improving organizational policy development for these structures. The novelty of the article is in the aspect of improving approaches to university structures optimization considering modern challenges and external environment changes, as well as justification of the need for different models of university organizational design depending on their mission and role I the social and economic development of regions and branches. The article if or interest for experts, researchers and practitioners in the field of university structure design.