The self-assemblies of three barbituric acid compounds on highly oriented pyrolytical graphite surface were investigated using scanning tunneling microscopy. On graphite surface, 5-(4-N-hexadecylaminobenzylidene))-2,4,6-(1H,3H)-pyrimidinetrione (BA I) pairs together with head–head styles and forms chiral structure with grouping of three molecular pairs as a unit motif. 5-(4-(N,N-Dihexadecylaminobenzylidene))-2,4,6-(1H,3H)-pyrimidinetrione (BA II) also appears as head–head molecular pairs but with slight displacement between each other. The small shift destroys the symmetry of molecular pairs and introduces chirality to the molecular pairs and in turn the formation of chiral domains. In this dense packing arrangement, only one hexadecyl chain of BA II lies on graphite surface, whereas the other one hangs in air. 5-(4-(N-Methyl-N-hexadecylamin obenzylidene))-(1,3-diethyl)-2-thioxodihydro-4,6-pyrimidinedione (BA III) organized into similar structure to BA II. Single molecular lines of BA III could be found in experiments from time to time, which suggests the weak intermolecular interaction due to structure changing in head part of BA III. These results may help us to understand varied self-assembling structure and process involved BA derivatives and other lipid molecules.