The digitalization of economic relations determines the particular importance of personnel training on a qualitatively new technological basis, which is inextricably linked with the study of the problem of ecosystem designing for the development of universities in a digital environment. The foundations of the systems theory, the theory of education economics, the methods of system analysis, factor analysis, and economic and mathematical modeling were used for studying the problem of ecosystem development for universities. The conducted studies made it possible to obtain the following main research results: the ecosystem principles for organizing the provision of higher education services, representing the integrity of the university system based on network interactions of a set of various participants, as well as objects, projects, processes, and environments, were proposed. An approach to designing a strategy for the development of universities, based on the scenario forecasting of the receptivity of digital economy competencies by students, teachers, and partners of universities in the medium term, is proposed based on the organigram for the implementation of the project of matrix digital transformation of the adhocratic university hierarchy. The conclusions stating that the design of the ecosystem of the development of universities should be aimed at the implementation of the social mission of the university in the region and the transformation of the ecosystem of the region as a whole are formulated. As prospects for further research, the study of the prerequisites for generating the effects of designing the development of a university ecosystem based on the network platform interaction of the economic agents of the region/territory, as well as the implementation of digital transformation projects of the university management system, is considered.