We carried out the nanoindentation simulations for the Ru (superlayer) / Cu (film) / SiO2 (substrate) system using the finite temperature MD-FEM coupling method. The calculations are performed for the different adhesion energies of Cu/SiO2 ranging from 0.2 to 0.6 J/m2. During loading, it was found that the interfacial crack nucleation occurs at three to four times the contact radius, driven by the tensile stress acted on the Cu/SiO2 interface. We also show that the asymmetric defect behavior have a great effect on giving birth to the crack nucleation. The observation of our simulation indicates that the mechanism of the crack nucleation strongly depends on the interfacial bonding energy.