Molecular dynamics (MID) simulation and the experiment of adhesion force measurement were introduced to study the nanostructure formation process in the atomic force microscopy. The atomic level process of the nanostructure formation and the thermo-mechanical effect caused by the factors of the contact area, the adhesion force, and the temperature were clearly shown and discussed. The size of the forming nanostructures was found to be positively related to the contact area and temperature, but the adhesion force would decrease as the temperature increase. In the case of higher temperature with smaller adhesion force, however, the larger-size nanostructure could still be made.