The thermal conductivities of mesogenic epoxy (ME) resin films were evaluated by thermal microscopy (TM) based on periodic heating thermoreflectance. A three-layer model, consisting of a glass layer to ensure surface planarity, a Mo layer to generate thermal reflectance signals, and a resin layer as the target for thermal measurement, was used in the analysis. The results revealed that the effective thermal conductivity increased upon decreasing the modulation frequency, reflecting the contributions from film regions at different depths. This behavior indicated a correlation between molecular orientation and thermal transport, which was consistent with the results of the previous reports on ME ordering. This method was also found to be suitable for materials such as polymers, adhesives, and soft substrates, on which direct Mo deposition was not appropriate because of possible thermal damage, or for those facing difficulties in achieving mirror-like surfaces required for TM.