The disjoining pressure is an important physical property in modeling the small-scale transport phenomena on thin film. It is a very useful definition in characterizing the non-continuum effects that are not negligible in heat and mass transport of the film thinner than submicro-scales. We present the calculated values of disjoining pressure of He, Kr and Xe thin films absorbed on graphite substrate using Molecular Dynamics Simulation (MD). The disjoining pressure is accurately calculated in the resolution of a molecular scale of the film thickness. The characteristics of the pressure are discussed regarding the molecular nature of the fluid system such as molecular diameter and intermolecular interaction parameters. The MD results are also compared with those based on the continuum approximation of the slab-like density profile and the results on other novel gases in the previous study. The discrepancies of the continuum model with MD results are shown in all three configurations and discussed in the view point of molecular features.