This article analyzes the issues of implementation of innovations and respective methodology of teaching humanities in universities. The aim of this article is to reveal challenges related with implementation and use of advanced innovative methods of teaching humanities in universities. This work substantiates the concept that modern processes occurring in education are direct consequence of complicated and deep transformations in culture, economy, policy of the World. Adaptation of life to wide-scale transformations is impossible without holistic comprehension of motives, trends and prospects of further social development, including education. The novelty of the work is in development of certain theoretic models of education development, which is rapidly moving away from the differentiation and fragmentation of scientific disciplines, modules and is concentrated on their integration. Another novelty in the existing paradigm of education can be presented by targeting of potential not just on distance methods but on creation of innovative education systems based, for instance, on technologies of virtual reality (VR). This work proves that in VR the educational components or prototypes can be presented by such units as virtual laboratory (workshop), lecture spaces, displaying of considered entities, network educational establishments.