Molecular dynamics (MD) calculations are used to study the contact behavior of self-assembled monolayer (SAM) deposited on gold substrate in dip-pen nanolithography (DPN). The interaction of SAM atoms was described by a general universal force field, the tight-binding, second-moment approximation was used for Au substrate, and the Lennard-Jones potential function was employed to describe interaction between the SAM and the Au substrate atoms. The MD model consists of a planar Au substrate with n-hexadecanethiol SAM chemisorbed to the substrate. When the SAM clusters are brought closer to the substrate surface, the interaction normal force is induced. The normal force increases as the size of SAM clusters increases. In addition, the effect of the temperature and the size of SAM clusters on the contact angle between the alkanethiol SAM and the Au substrate in DPN are evaluated. Results show that the contact angles decreased as the temperature increased, and the smaller the cluster size, the smaller the contact angle.