The authors of the article analyze the prerequisites, conditions and directions of humanities-based knowledge transformation which provide the implementation of educational innovations in a research university. The first part of the article presents the organizational and implementational principles for innovation-oriented educational research. The principles are based on the comparative analysis of ethnomethodological, conversation and microethnographic approaches. The second part of the article focuses on case study method which can be adapted to the objectives of university’s innovative development. Such adaptation allows to specify university’s constitutives, forms of its application and parameters for evaluating its effectiveness.