At the head of the Institute are the Academic Council and the Director.

IMEMO has the following research departments:

 Department of Science and Innovation
 Department of Global Economic Problems and Foreign Economic Policy
 Department of Modern Market Economy Theories
 World Economy Forecasting Section
 Department of International Capital Markets
 Center for Industrial and Investment Studies
 Center for Energy Research
 Center for Research in Transitional Economies
 Agribusiness Center
 Group for Analysis of Price formation, Inflation and Taxation
 Section of Economic Modeling
 Department of International Politics
 Theory of Politics Section
 Center for International Security
 Center for North American Studies
 Center for European Studies
 Department of European Political Studies
 Center for Asia Pacific Studies
 Center for Development and Modernization
 Center for Comparative Socio-Economic and Socio-Political Studies