The author gives his contribution to the solution of important problems related to the setting of an organization theory of complex systems and shows the applications resulting from it in important fields of knowledge, such as biological, the psychological and sociological. He shows how traditional concepts of science are upset. In particular, certain results of Clausius in thermodynamics and of Boltzmann in statistical physics, the formulation of the problem of the order formation in isolated systems, the theory of the galaxies formation, certain aspects of the theory of evolution, the organization of the immune system, then important aspects of psychic and social systems.