High temperature superconducting (HTS) transformers have many advantages over conventional transformers in terms of volume, weight, and total efficiency. However, fault conditions limit the electro-thermal performance of an HTS transformer. Based on this, we investigate the thermal modeling of the HTS transformer in the fault-current state. For thermal modeling, heat transfer and parameters affecting it such as surface roughness and bubble behavior have been considered. At first, an accurate thermal model for a 10 kVA HTS transformer has been prepared. Experimental results show that the penalty of this model is about 2.5 K in the hot-spot point (HSP) temperature in fault-current conditions. In a second step, the impact of a roughness on the heat transfer and mass transfer rate in nucleated boiling mode is investigated. Results show that surface roughness decreases the HSP temperature by more than 10 K in fault-current conditions. These results have significant impacts on protecting HTS windings against quenching.