The carbonaceous material possesses many kinds of structures and extensive applicability. For example, they are used for lithium battery and fuel cell electrode, printer¡¦s carbon powder, and for the reinforcement of tire. The carbon nanotube and carbon nanocapsule are the novel carbonaceous materials. Their unique property and applicability have attracted a lot of investigation. In this research, we attempt to understand the relationship between the structures and chemical properties of the carbonaceous material. Graphite is an ideal model for this study, and the temperature-programmed desorption method is applied in this investigation. XRD and TEM are also used to support the results of TPD method. Four kinds of exploration molecules are chosen. They are benzene-like molecules, cyclohexane-like molecules, long chain molecules and alcohol-like molecules, respectively. We attempt to find out the differences of the interaction between graphite and various kinds of molecules. The benzene-like molecules with alkyl branch are strongly adsorbed on graphite. The adsorption of long chain molecules on graphite is the next. There are more than one kind of adsorption site on graphite available for 1,3-hexadiene and alcohol-like molecules adsorption. The adsorption behavior of 1,3-hexadiene and alcohol molecules are more complicated. Although the desorption activation energy for different molecules on graphite with different coverages are different. The difference in the desorption activation energy are negligible. The tendency of change is similar for the same kind of molecules. The adsorbed molecules can also diffuse into graphite¡¦s interlayer structure. The interlayer distance of graphite can be changed by the diffusion process of the adsorbed molecules. The desorption activation energies may change when graphite¡¦s pore size changes or functional groups exist on graphite surface. The changes of the activation energy caused by the change of graphite¡¦s pore size or by the surface functional groups are more prominent than the changes induced by the coverage difference of adsorbed molecules on graphite.