A system and method for computing thermal boundary conditions from an unstructured computational fluid dynamics (CFD) simulation for a thermal simulation of a structural component are disclosed. The thermal boundary conditions include convective heat transfer coefficient (HTC) and reference temperature (Tref). In one embodiment, prism cells are formed to capture boundary layer substantially next to a wall of the structural component. Further, tetrahedral cells are formed to capture a diffused temperature layer substantially next to the formed last prism cell and in a direction normal to the wall. Furthermore, temperature of each of the prism cells is computed in the direction normal to the wall until a substantially first tetrahedral cell. In addition, the computed temperature of the prism cell that is substantially adjacent to the first tetrahedral cell is declared as the Tref. Also, the HTC is computed using the obtained Tref.