The article presents methodological principles of training of future philosophy doctors for research and innovation activity, based on four levels of methodology: philosophical, general scientific, specifical scientific and technological. Each of the levels represents a system of methodological approaches and principles. The philosophical basis of the study is a combination of the general provisions of the theory of cognition, philosophical conceptions of activity and its connection with consciousness and personality, philosophical interpretation of creativity, philosophical concept of reflexivity, and philosophical vision of the relationship between theory and practice, as well as the principles of objectivity, development, universal communication. The general scientific level is represented by systematic and synergistic approaches, which are specified in the principles of systematicity, integrity, discretion, modelling, emergence, nonlinearity, and openness.At the specific scientific level there are distinguished such methodological approaches as: activity, personality-oriented, competence-based, acmeological, axiological, project-technological.The approaches are revealed through the general pedagogical principles: scientific, systematic and consistent, combining different methods, learning methods activity, learning through action, gradual mastery of activity, productivity of learning, organization of joint activity, communication of training with practical activity, humane isolation, voluntariness, polysubjectivity, variability, individualization and differentiation, collaboration and creativity, integration of formal, non-formal and informal education, lifelong learning, self-development orientation. The technological level involves the use of andragogical, contextual, environmental, socio-cultural, creative and reflective approaches, as well as a number of specific didactic principles: problematicity and reflection, critical self-assessment, innovation, regionality.