Formulation of the problem. Optimal design of avionics (avionics) structures is impossible without the development of new complex methods for modeling thermal processes in their designs and verification based on the results of a full-scale experiment, as well as the creation of methods for the justified use of existing and creation of new mathematical algorithms for optimization procedures. When designing modern RES, it is important to provide a temperature regime for the functioning of power elements of the equipment, in our case, we will consider an electronic module. To ensure normal thermal conditions, cooling systems are used, most often heat sinks (radiator) are used, but in some cases it is not possible to install it. To solve this problem, it is proposed to develop a liquid and air cooling system for the electronic module using an expanded set of elements of cooling systems, including a submersible cooling system. Purpose. Develop a comprehensive methodology for modeling and optimal design of a liquid cooling system for an electronic module, the reliability of which is confirmed by the results of analytical calculations and experimental data. Results. On the basis of the developed 3D model of the electronic module, the procedures for multivariate analysis of the laboratory stand unit were implemented using modern computer-aided design tools. A mathematical formulation was formed and procedures for optimizing the thermal regime were performed: modeling and optimization of the coolant; block topology optimization; optimization by body material and coolant type. Graphs and tables of simulation results are presented, on the basis of which it is possible to draw conclusions about the influence of a particular parameter on the distribution of heat fluxes. All the difficulties that the authors encountered in the course of design optimization in the modeling environment are described in detail, as well as ways to solve them. Practical significance. The results obtained make it possible to apply the proposed method for numerical simulation of thermal processes in REM designs, verification based on the results of a full-scale experiment, as well as the creation of methods for the justified application of existing and the development of new mathematical algorithms for optimization procedures.