The article discusses the features of the educational process organization in the postgraduate study of a scientific research institute (SRI) with the example of the Joint Stock Company “Vedeneev All-Russia Research Institute of Hydraulic Engineering". A comparison is drawn on the organizational and methodological aspects of the postgraduate course at a research institute and a technical university. The annually updated curriculum is analyzed, which provides a multilevel system of academic disciplines, with horizontal and vertical interdisciplinary links. A matrix of competence descriptors and academic disciplines conjugation is presented. It is shown that postgraduate studies at the research institute allows to build a model of research education for postgraduate students, which requires the choice of an optimal educational trajectory by means of the inclusion in the curriculum of academic disciplines of the corresponding special focus and the establishment of strong interdisciplinary links. A competence-based approach aimed at developing universal, general professional and professional competences in research and teaching activities in postgraduates, as well as a personality-oriented approach, assuming the focus of the educational component on the personal development of graduate students, is taken into account. The organization of practice and research work (R&D) of a graduate student is considered in detail. It is shown that the availability of the material and technical base in the research institute provides a broad practical training of graduate students, taking into account training individualization and the implementation of theoretical training.