The production of any multilayer structure begins with the development of technological documentation, which describes, among other things, the temperature regimes during their manufacture. Conventionally, the temperature process of polymerization can be divided into three stages: preheating, temperature stabilization and cooling. The paper presents the results of a numerical calculation of temperature fields in a multilayer composite structure with a honeycomb filler during its manufacture by autoclave molding at the preheating stage. This method of manufacturing composite structures makes it possible to mold parts of varying complexity and dimensions, the demand for which is growing in such industries as mechanical engineering, aircraft building, and shipbuilding. The requirements for the quality of such products are increasing, which is greatly influenced by compliance with the temperature regime during molding. Conducting direct experiments requires large energy costs, therefore, to solve the problem of controlling heat exchange processes inside the structure, mathematical models were developed that describe these processes. A non-stationary heat conduction problem is formulated for a multilayer unbounded plate with a constant initial distribution, boundary conditions of the third kind on the outer boundaries, and boundary conditions of the fourth kind on the contact surfaces of the layers. Using the finite element method, the problem is reduced to three-point difference equations, the solution of which is found by the sweep method. The determination of the sweep coefficients is shown taking into account the thermal characteristics of the layers. The results of a numerical calculation of the temperature distribution for a nine-layer composite structure with a honeycomb core are presented. The numerical calculation was carried out using the developed program in the BorlandDelphi 7.0 object-oriented programming environment. The results obtained are presented in the form of graphic dependences of the temperature over the thickness of the sample at different points in time, as well as the dependence of temperature on time at various nodes of the sample in comparison with the theoretical curve. An analysis of these dependences was carried out, which showed that the heating of the sample occurs unevenly over its thickness. The deviation from the theoretical temperature values is observed in the layers located closer to the honeycomb layer. This can adversely affect the course of the polymerization step, which is characterized by the conversion of the binder into a polymer, and occurs at certain temperatures. Therefore, achieving the desired temperature values at the stage of heating the structure is important for the manufacture of reliable and durable structures that can withstand extreme operating conditions. The obtained temperature distributions make it possible to correct the technological process of manufacturing various multilayer structures at the stage of its development, which will reduce the economic costs of production.