<p>This study employed molecular dynamics simulation to systematically investigate the effects of different cooling rates on the atomic microstructural evolution of Al–Fe binary amorphous alloy models. Results demonstrated that the cooling rate significantly influences the Voronoi volume, coordination number, atomic bond proportions, and atomic arrangement of Al–Fe binary amorphous alloys. Atomic bond proportion analysis indicates that despite the relatively weak thermodynamic driving force for bond formation between dissimilar atoms under low mixing enthalpy (− 11&#xa0;kJ/mol), the cooling rate significantly affects the distribution of Al–Fe, Al–Al, and Fe–Fe bonds. Under low cooling rates, the atoms have ample opportunities for rearrangement and diffusion, resulting in a reduction in Voronoi volume and an increase in the number of icosahedral clusters. At the same time, the proportion of Al–Fe bonds significantly increases, and those of Al–Al and Fe–Fe bonds decrease, thereby promoting the formation of a dense and ordered structure in the system. This microstructural evolution is directly reflected in the increased Young’s modulus of the model at low cooling rates.</p> Graphical abstract <p></p>