In this paper, a method for molecular dynamics simulation of polycrystalline copper is proposed. Atoms of polycrystalline copper are placed in a simulation cell in accordance with the face-centered cubic lattice. Then the system is heated above its melting point under pressure equal to the atmospheric pressure. The melt obtained is cooled abruptly to the temperature range from 400K to 1200K under the atmospheric pressure. After that, the atomic system evolution at constant temperature leads to homogeneous nucleation of copper crystallites with the growth time of several tens of nanoseconds and results in polycrystalline sample formation. Based on the results of molecular dynamics study of uniaxial deformation, the yield stress increase with the grain size decrease from 14 nm to 6 nm in accordance with the Hall-Petch relation is shown. Further decrease of the grain size leads to the yield stress decrease due to the change of microscopic deformation mechanism. Young’s modulus decrease is observed for polycrystalline copper with the grain size less than 10 nm.