The European Union (EU) is a challenge both for the actual political processes and conducting theoretical deliberations seeking interpretations adequate for this structure. The premise that constitutes the starting point for the article is a perspective of the EU as a complex integration system that goes beyond the formula of typical international cooperation. The degree of complexity of this system strongly affects thepossibilities of implementation and the pace of system changes. Among the factors influencing the aforementioned processes are modernization, understood as the implementation of new solutions that improve cooperation and crises hindering the progress of the integration process and that accompany the development of European integration from the very beginning. The perspective of complex adaptation systems allows to adopt an approach that enables understanding the specificity of the penetration of crisis and modernization factors in the EU.