We present a microscopic theory of the second order phase transition in an interacting Bose gas that allows one to describe formation of an ordered condensate phase from a disordered phase across an entire critical region continuously. We derive the exact fundamental equations for a condensate wave function and the Green functions, which are valid both inside and outside the critical region. They are reduced to the usual Gross-Pitaevskii and Beliaev-Popov equations in a low-temperature limit outside the critical region. The theory is readily extendable to other phase transitions, in particular, in the physics of condensed matter and quantum fields.