In recent studies, lipid bilayers attract a great deal of interest as a material for nanoscale structure. Some devices utilizing lipid bilayers, which include various kinds of sensors and molecular sorting devices, have been proposed. Understanding of thermal energy transfer in the lipid bilayers plays an important role in developing such devices with nano structures. In this study, we have investigated the energy transfer along and across the bilayer membrane by molecular dynamics simulations of the lipid bilayer in liquid water. We found that along the bilayer, the thermal energy is transferred by the interaction principally between water molecules and barely between lipid molecules. On the other hand, in the latter case, total thermal resistance of the lipid bilayer structure is composed of the thermal resistance of the structure's various parts, including water, head group of lipid, and tail hydrocarbon chain of lipid, which show different values. It is found that the tail hydrocarbon chains have the highest thermal resistance.