This paper attempts to provide a theoretical basis for the EU crisis on the development of integration in the past decade (2009 to 2019). First, it analyzes neo-functionalist integration theory, and the revision and amendment thereof, with reference to the concepts of new institutionalism and constructivism. Second, three main gaps are apparent in multiple EU crises—between commitment and implementation, between elite and public opinion, and between a European and national identities. Third, arguments are offered on the factors which caused the EU crisis on the basis of the theory of amended neo-functionalism. The final part concludes the EU crisis had its origins in the divergence between interest distribution and identification.