Abstract Multilayer materials have been widely used in engineering applications, attributed to excellent thermo-mechanical performances. However, the thermal or mechanical properties of multilayer materials remain elusive, owing to contact behaviors etc. factors. In order to address this issue, an innovative method is employed to estimate the effective thermal conductivity (ETC) of multilayer materials considering thermal contact resistance (TCR) between layers, and the equivalence performance is investigated by solving three-dimensional inverse heat conduction problems. First, the equivalence method is validated by available experimental data of a multilayered insulation composite material. Then, the precision of different equivalence methods is compared, and the results indicate that the anisotropic equivalence method has higher accuracy than the isotropic and orthotropic equivalences for the five-layer material in the present work. Finally, the robustness and stability of the anisotropic equivalence method are evaluated in detail. The present work provides a new alternative method for predicting the effective thermal conductivity of multilayer materials.