Using a coarse-grained molecular dynamics simulation based on the bead-spring polymer model, we reproduced the film distribution of molecularly thin lubricant films with polar end groups coated on the disk surface and quantified the film-surface morphology using a molecular-probe scanning method. We found that the film-surface morphology changed periodically with increasing film thickness. The monolayer of a polar lubricant that entirely covers the solid surface provides a flat lubricant surface by exposing its nonpolar backbone outside of the monolayer. By increasing film thickness, the end beads aggregate to make clusters, and bulges form on the lubricant surface, accompanying an increase in surface roughness. The bulges continue to grow even though the averaged film thickness reaches or exceeds the bilayer thickness. With further increases in film thickness, the clusters start to be uniformly distributed in the lateral direction to clearly form a third layer. As for the formation of fourth and fifth layers, the process is basically the same as that for the second and third layers. Through our calculations of the intermolecular potential field and the intermolecular force field, these values are found to change periodically and are synchronized with the formation of molecule aggregations, which explains the mechanism of forming the layered structure that is inherent to a polar lubricant.