In this paper, the deposition of the carbon atoms on a graphene layer has been investigated by the molecular dynamics simulation in the canonical ensemble at finite temperature. In this simulation we use Brenner potential model for interaction between carbon atoms in the graphene layer and Lennard–Jones of Van der Waals potential model for interaction between carbon atoms (gas) and also between carbon atoms (gas) with the graphene layer. In the process of deposition, aggregation and random distribution of carbon atoms on graphene layer lead to produce a rough surface. We study the behavior and changes of the surface roughness as a function of temperature. Finally, we found that the increasing of temperature increase the surface roughness.