The paper advocates the Bogoliubov method of quasi-averages for quantum systems. First, we elucidate its applications to study the phase transitions with Spontaneous Symmetry Breaking (SSB). To this aim we consider example of Bose-Einstein condensation (BEC) in continuous systems. Our analysis of different type of generalised condensations demonstrates that the only physically reliable quantities are those that defined by Bogoliubov quasi-averages. In this connection we also give a solution of the problem posed by Lieb, Seiringer and Yngvason in [SY07]. Second, using the scaled Bogoliubov method of quasi-averages and taking the structural quantum phase transition as a basic example, we scrutinise a relation between SSB and the critical quantum fluctuations. Our analysis shows that again the quasi-averages give an adequate tool for description of the algebra of critical quantum fluctuation operators in the both commutative and noncommutative cases.