The article presents a theoretical analysis of the ecosystem approach as a methodological basis for innovative transformations in higher pedagogical education. The essence of the ecosystem approach in education is to direct the researcher to a systematic vision of the relationships and processes necessary to maintain ecological (healthy, sustainable, productive, diverse, coordinated) human relationships within and outside the educational system, its integrity, elements and structures, functions, values and qualitative parameters of life through self-regulated management, protection and preservation of educational ecosystems over time. The author of the article analyzes the scientific thesaurus of the problem, the essence and origins of the ecosystem approach, its conceptual basis and basic axioms, the main aspects, basic principles and ways of implementing the ecosystem approach in higher education. Particular attention is paid to educational ecosystems as a key driver of innovative development of higher pedagogical education. In particular, the article examines the nature, features, characteristics and basic approaches to the development of educational ecosystems (ecosystem as belonging and ecosystem as structure), considers the peculiarities of their formation and development depending on the structure. A scientific thesaurus of the problem of developing an ecosystem of higher pedagogical education is presented. It is represented by such concepts as: «ecosystem approach», «ecosystem structure», «ecosystem actors», «ecosystem constellation», «ecosystem life cycle». The stages of development of educational ecosystems are summarized and the advantages of implementing the ideas of the ecosystem approach in a modern university (improving the efficiency of the educational process, increasing the accessibility of education, improving the quality of education) are considered. The materials of the article can be used to develop effective tools for the support and innovative development of educational ecosystems in higher education institutions