The results of the study contain methodological approaches to assessing structural factors affecting the development of the economy. The interrelation of structural deformations and entropy processes affecting the stability of the economic system and the economic security of the state is revealed. The features and economic parameters of countries with economies in transition are revealed, in which the sectoral and technological structure of the economy, the proportions of the balance of payments and trade balance are radically changing; structure of exports of goods and services; employment structure. The concept of "structural entropy" has been introduced into scientific circulation, which characterizes the narrowing of the sectoral structure of the economy and a decrease in synergetic opportunities for economic development. The reasons for the weakening of links between the elements of the economic system and the impact of structural deformations on the economic development of countries with economies in transition are considered. The analysis of the possibilities of economic development of these countries within the framework of regional integration is carried out, an assessment of the convergence of countries belonging to regional unions is carried out. The structural conditions of economic evolution and convergence are substantiated. Recommendations were developed for the formation of institutional and innovative mechanisms to ensure positive structural changes in the national economy. The proposals aimed at counteracting structural deformations and increasing the synergistic potential of systems are presented.