The history of the CIS as a territory of the former Soviet republics and as an association of new independent states appears as a search for new meanings of this space and a model for integrating new subjects of this space in a radically changed economic and geopolitical conditions. The chronology of the integration processes in the post-Soviet space shows that new integration projects overshadowed the old ones, which led to problems of matching integration projects in the context of their further development. Existing integration projects involve the establishment of coordination of national development goals developed by countries; however, national interests inevitably prevail on the path of integration, which gives rise to contradictions that manifest themselves both in natural historical gravity and in defending national interests related to the protection of the acquired sovereignty. In the course of the study, it was revealed that the development and transition to its own model of integration should take into account the strong differentiation in terms of the level of economic development of the integrating countries. The presence of prerequisites for the implementation of the neo-functional concept of “spillover” in the form of the creation of supranational bodies, although it is a necessary condition, the very existence of supranational institutions is not sufficient to deepen integration through the “spillover”. The study examines the reasons why there is no deepening of integration and touches upon the problems of conjugation of the integration projects of the CIS and the EAEU. It is concluded that the further integration of the EAEU to a lesser extent correlates with B. Balashi's particular classical linear-stage model. The conditions of strong economic differentiation of new independent states and political contradictions that play a significant role in cross-border cooperation determine the search for integration models other than the EU, which would meet the criteria for strong differentiation of integration participants with deepening integration without supranational regulatory bodies.