In this study, molecular dynamics simulations have been used to study the influencing factors, such as the time of each heating step, temperature, and annealing time, on the structure and crystallization process of Cu–Au alloy. The results show that when the temperature increased, the crystallization process decreased, and the structure gradually turns to the liquid state, and vice versa. When increasing the time of each heating step and the annealing time, the crystallization process increased, then increased the most at the glass temperature, Tg = 550 K. During the phase transition, link length (r), total energy (Etot), size (l), number of FCC, HCP, and Amor structural units have a significant change. The obtained results of Cu-Au alloy can serve as a basis for future experimental studies.