Nano-size Cu precipitates are the main products of irradiation embrittlement of nuclear reactor pressure vessel steels. Molecular dynamics simulation within the framework of embedded atom method is performed to study atomic packing change in Fe-Cu binary system, where the small Cu clusters are embedded in the crystal body centered cubic (BCC) Fe lattices. As the temperature increases, atomic packing change occurs in the Fe-Cu binary system. The mean square displacement of Cu atom, pair distribution function of the Cu atoms, and the atomic density profile along the radial direction are calculated. The atom packing structures in pure Cu region, Fe-Cu interface region, and pure Fe matrix are analyzed. The simulation results show that the packing structures in the Cu cluster and the Fe matrix are greatly affected by the sizes of these clusters and the volume of the Fe matrix containing these clusters. The structural changes present apparent differences, for the Fe matrixes contain these confined Cu clusters with different atom numbers during heating. As the Fe matrix can only provide small space to accommodate the Cu atoms, packing patterns in many Cu atoms are disordered for the Febulk-Cu135 system. In this binary system, strain region in the Fe matrix is adjacent to the Cu cluster. In the meantime, there are a lot of vacancy defects and strain regions in the matrix. For the Febulk-Cu141 system, although the Cu cluster contains more atoms, the Fe matrix can accommodate Cu atoms in a larger space, and the majority of these Cu atoms are located at the BCC crystal lattices. With increasing the temperature, the changes can be observed that the number of the strain regions decrease, whereas the sizes of some strain regions increase.