A Nd:YAG laser operating at a wavelength of 266 or 355 nm is used to deposit a thin layer of copper on the (0 0 0 1)α-Al2O3 surface. The formation process is precisely controlled by identification of time distribution of two characteristics: energy and flux density of particles incident on the substrate. For this purpose, the Cu-plasma expansion is described by means of an analytical hydrodynamic model whose self-similar solutions are fitted to the experimental plasma images and time-of-flight spectra. The obtained nanocomposite is examined by the aberration-corrected high-resolution transmission electron microscopy (Cs-HRTEM) method. The results reveal that copper crystals assume one main orientation relative to the substrate (1 1 1)[2 −1 −1]Cu$‖$ ‖ (0 0 0 1)[−1 −1 2 0]α–Al2O3 and the formed interface has a specific microstructure. To reconstruct the phase boundary region, molecular dynamic (MD) and static (MS) simulations are carried out. The results show that strong bonding between copper and sapphire induces structural changes in the (1 1 1) Cu layer nearest the substrate and leads to formation of the system of partially dissociated dislocations in the next layer. In consequence, the Cu/α–Al2O3 interface becomes the semicoherent system. The lattice matching regions of the individual Cu layers are significantly lowered, which results in strong deformations along the closed packed planes. The reconstructed interface is used for Cs-HRTEM image simulation. A good accordance with the experimental results indicates that the MD model correctly maps the microstructure at the phase boundary of the synthesized nanocomposite.