Understanding of the defect evolution mechanism under irradiation is very important for the research of pressure vessel steel embrittlement. In this paper, the embedded atom method (EAM) based canonical ensemble molecular dynamics (MD) method was used to study the evolution of the stacking structure of different nano-sized Cun (n = 13, 43 and 87) clusters in an Febulk embedded with BCC lattice structure during continuous heating. The mean square displacement, pair distribution functions and atomic structures of Cu atom clusters at the nanometer scale were calculated at different temperatures. The structural changes present apparent differences, for the Febulks contain nano-sized Cu clusters with different atom numbers during heating. For the Febulk–Cu13 system, since the ability to accommodate the atomic Cu in the Fe substrate is lesser, a small number of Cu atoms in BCC lattice positions cannot influence the whole structure of the Fe-Cu system. For the Febulk–Cu43 system, with an increase in temperature, a Cu atomic pile structural change happened, and the strain areas decreased significantly in the Febulk, but a single strain area grew large. For the Febulk–Cu87 system, when the Cu atoms are constrained by the Fe atoms in bulk, only a few of the Cu atoms adjust their positions. With the increase in temperature, strain in the Fe eased.