For the development of functional thin films with high thermal conductivity, the local ordering structure of a cured liquid crystalline epoxy resin (LCER) droplet was investigated by using synchrotron radiation microbeam small-angle X-ray scattering. The cured LCER in the vicinity of a substrate with low surface free energy was revealed to form a polydomain smectic-A (SmA) structure in which the normal direction of the layers was random in each domain, although the alignment was planar near the air interface. On the other hand, the cured LCER on a substrate with high surface free energy formed a homeotropically aligned SmA structure in the region within 21 μm from the surface of the substrate. Therefore, a 20 μm thick LCER film was fabricated and found to form a homeotropically aligned monodomain-like SmA structure throughout the whole film with a high thermal conductivity (0.81–5.8 W m–1 K–1). This film with a high thermal conductivity is expected to be applicable for adhesion and precoating materials for electrical and electronic devices.