To investigate structural changes, the Cu95Fe5 alloy system was subjected to cooling rates of 1 × 1013 K/s, 2 × 1012 K/s, 2 × 1011 K/s, and 2 × 1010 K/s using the molecular dynamics simulation method. The results revealed that decreasing the cooling rate caused an increase in the phase transition temperature. Further, the structure of the alloy system exhibited a tendency towards increased stability following cooling at lower cooling rates. The Fe precipitation behavior of the Cu95Fe5 alloys during cooling at the rate of 2 × 1010 K/s was further explored, with the results suggesting that the formation and growth of the Fe cluster is a continuous process governed by the nucleation and growth mechanism. The size and number of Fe clusters formed at different stages were found to be affected by three factors, namely, the interaction force between the Fe atoms, the diffusion ability of the Fe atoms, and the interfacial energy between the Fe cluster and Cu matrix. When the alloy temperature exceeded 1400 K, the accumulation of the Fe atoms was facilitated by their strong interaction. However, the high temperatures and the large diffusion coefficient of the Fe atoms acted as inhibitors to the growth of Fe clusters, despite the intense thermal activities. As the temperature was reduced from 1400 K to 1050 K, the Fe atoms moved with a reduced intensity in a narrower area, and both the number of Fe atoms in the largest cluster and the number of clusters increased due to the action of the interaction force between the Fe atoms. Upon lowering the temperature from 1050 K to 887 K, the size of the largest Fe cluster increased rapidly, while the number of clusters decreased gradually. The growth of the largest Fe cluster could be partly attributed to the diffusion of single Fe atoms into the cluster under the action of the interaction force between the Fe atoms, in addition to the gathering and combination of multiple clusters. When the temperature was lowered from 967 K to 887 K, the diffusion coefficient of the Fe atoms approached 0, indicating that the non-diffusive local structure rearrangements of atoms dominated in the system structure change process. The interface energy governed the combination of the Fe clusters in this stage. At a temperature below 887 K, the alloy crystallized, the activities of the Fe atoms were reduced due to a low temperature, and the movement range of the Fe atoms was small at a fast cooling rate. As such, both the size and number of Fe clusters showed no obvious changes.