Now Russia lives in the conditions of reforming and the ongoing transformations, which creates new management conditions. The opportunity of using high technologies of the developed countries (for example, EU countries) that existed earlier is now missing in connection with the imposition of sanctions. The task to solve major strategic problems is now set for science, in particular, that of import substitution in the field of high technologies. Thus, the logic of developing globally competitive economic, innovative and economic processes proves that in modern conditions the main attention of the state has to be concentrated on developing the science, education and hi-tech sector of the industry on a platform of the concept of economy of knowledge. The article considers the tendencies in assessing the functioning of scientific and educational complexes both in Russia and abroad, and also the issues of managing the processes of import substitution in the sphere of high technologies within the activity of a scientific and industrial and educational complex in the conditions of reforming and modernization. The authors offer to use the well-proved methods and tools of economy of quality for solving the problems arising in modern conditions, allowing to estimate the overall activity with respect to the processes of a scientific and educational complex and to offer the possible directions of optimizing its activity and ensuring efficiency on the basis of the tools of economy of quality. The authors note that any country, including Russia, can become an advanced country with a high standard of living of the population only by continuously focusing on the problems of science and education, by creating a society of knowledge combining science, education and business, and also by applying effective methods and tools of economy of quality for assessing the functioning of a scientific and educational complex.