An important precursor 4,5-didodecylthiolph- thalonitrile (DCP) for synthesis of phthalocyanines (Pcs) and subphthalocyanines (SubPcs) was synthesized and the assembling structure of this molecule on the basal plane of highly oriented pyrolytic graphite (HOPG) surface was characterized using the scanning tunneling microscopy (STM) in ambient conditions. In high-resolution images of the molecules, we found that the arrangement of the cyano groups forms a "head-to-head" configuration to keep the stability of the entire system. The mismatch of the DCP molecules with the substrate lattice has also been observed in the experiment.