The subject of the article is the problem of the crisis of the Russian education system and, above all, the ideology and general methodology of teaching in the field of humanities. The purpose of the study is to formulate new principles as part of the author's methodology of training courses for higher education in the conditions of Russia's withdrawal from the Bologna process and the formation of a national educational system. The modern education system is the result of many trends in the development of society — and above all secularization, the separation of science from religion and the development of the positivist nature of scientific knowledge. The crisis of modern education is a manifestation of the crisis of positivist science and the global crisis. Russia was the first in the world among non-Muslim countries to publicly declare the rejection of liberal principles of social structure. The paper proposes a new methodology — moral and religious neo-institutionalism, containing three main principles — system, balance and morality. The latest practical result of its implementation is the launch of the publication of the INFRA-M publishing house of a series of books "Russian University Textbook on Economics and Management" intended for master's degree (advanced level). Among them the textbook "Economic theory. Russian Economics" took the first place in the international academic course "Academus" in the nomination "Economics and Management".