This paper investigates the crystallization process of FeNi alloys with different impurity concentrations of Ni(x) [x = 10% (Fe90Ni10), 20% (Fe80Ni20), 30% (Fe70Ni30), 40% (Fe60Ni40), and 50% (Fe50Ni50)] at temperature (T) = 300 K and Fe70Ni30 at heating rates of 4 × 1012, 4 × 1013, and 4 × 1014 K/s at different temperatures, T = 300, 400, 500, 600, 700, 900, 1100, and 1300 K. Molecular dynamics models with the Sutton–Chen embedded interaction potential and recirculating boundary conditions are used to calculate the molecular parameters of alloys, such as radial distribution function, total energy of the system (Etot), size (l), and crystallization temperature (through the relationship between Etot and T). The common neighborhood analysis method is used to confirm the theoretical results of crystallization for Fe–Fe, Fe–Ni, and Ni–Ni. The annealing process did not have an effect on the crystallization process of FeNi alloys. The effect of Ni content, heating rate, and annealing time on structural unit numbers, such as face-centered cubic, hexagonal close-packed, blocked cubic center, and amorphous, and the crystallization process of FeNi alloys is also investigated.