The molecular orientation effect of a liquid crystalline (LC) epoxy resin (LCER) on thermal conductivity was investigated, with the thermal conductivity depending on the surface free energy of amorphous soda-lime-silica glass substrate surfaces modified using physical surface treatments. The LC epoxy monomer was revealed to form a smectic A (SmA) phase with homeotropic alignments on the surfaces of substrates that possess high surface free energies of 71.3 and 72.7 mN m-1, but forming a planar alignment on the surface of a substrate that possesses a relatively low surface free energy of 46.3 mN m-1. The optical microscopy observations and the X-ray analyses revealed that the LC epoxy monomer also induced a homeotropically aligned SmA structure due to cross-linking with a curing agent on the high-free-energy surface. The orientational order parameter of the resulting homeotropic SmA structure was calculated from the grazing incidence small-angle X-ray scattering patterns to be 0.73-0.75. The thermal conductivity of the cross-linked LCER forming a homeotropically aligned SmA structure was also estimated to be 2.0 and 5.8 W m-1 K-1 for the average and maximum in the direction of the Sm layer normal. The value of the thermal conductivity was remarkable among the thermosetting polymers and ceramic glass, and the LCER could be applied for high-thermal-conductive adhesives and packaging materials in electrical and electronic devices.