To investigate the conformational features of individual organic molecules on the substrates, we synthesized 5-(4-methylthiophenyl)-10, 15, 20-tris(3,5-di-t-butylphenyl) porphyrin (MSTBPP) molecules. The conformation of MSTBPP molecules dispersed on an Au(111) surface was investigated using Frequency Modulation Non-contact Atomic Force Microscopy (FM-NCAFM) under UHV condition with nano-meter spatial resolution. It was found that the methylthiophenyl group of MSTBPP molecules enhances the attractive interaction between the molecule and the substrate, which works as an anchor to fix their relative position to the substrate. This function dominates their conformation and mobility on the substrate. These findings lead to various possible strategies to control the conformation of molecules on the substrate, which is one of the important keys to realize the supra-molecular devices.