One of the important directions in the field of creating new structural and functional materials is the study of materials with a complex structure and unique strength or temperature properties. Due to the heterogeneity of their structure, such materials are called “structurally sensitive”. The heterogeneity of the structure of such materials is justified by the technological features of their creation. Structurally sensitive materials can be obtained by compacting nanopowders, deposition on a substrate, etc. The paper considers a mathematical model of heat propagation in a composite rod. At one of the ends of the rod, a protective coating of structurally sensitive material is used. Using the finite element method, numerical solutions are found for a problem with conditions of ideal thermal contact of rod parts. The results of the numerical calculation for various materials are given. The influence of material parameters on the heat distribution in the rod is analysed.