Temperatures of engine head and liner depend on many factors such as spray and combustion process, coolant passage flow and engine related structures. To estimate the temperature distribution of engine structure, multi-dimensional computational fluid dynamics (CFD) codes have been mainly adopted. In this case, it is of great importance to obtain the realistic wall temperature distribution of entire engine structure. In the present work, a CFD-FEM coupling methodology was presented to address this demand. This approach was applied to a real large-size marine diesel engine. CFD combustion and coolant flow simulations were coupled to FEM temperature analysis. Wall heat flux and wall temperature data were interfaced between combustion simulation and solid component temperature analysis via translator by a commercial CFD package named FIRE by AVL. Heat transfer coefficient and surface temperature data were exchanged and mapped between coolant flow simulation and FEM temperature analysis. Results indicate that there exists the optimum cell thickness near combustion chamber wall to reasonably predict the wall heat flux during combustion period. The present study also shows that the effect of cell refining on predicting in-cylinder pressure during combustion is negligible. Hence, the basic guidance on obtaining the wall heat flux needed for the reasonable CFD-FEM coupling analysis has been established. It is expected that this coupling methodology is a robust tool for practical engine design and can be applied to further assessment of the temperature distribution of other engine components.