Nanoindentation has been utilized to investigate the variations of the interatomic distances in both the initial and bulk states of the β-Al3Mg2, ε-Al30Mg23 and γ-Al12Mg17 phases. This technique has enabled the identification of the properties of these phases throughout the process. Continuing previous nanoindentation simulations conducted on the same phases [1], this study aims to further understand the behavior of these materials under molecular dynamics along the [001] direction. A proportional relationship between the applied load and atomic displacement affects the pair-wise distance, depth, and penetration amplitude for the three phases. Among them, the ε-Al30Mg23 phase demonstrated the greatest depth and amplitude of deformation compared to the β-Al3Mg2 and γ-Al12Mg17 phases. Interatomic distances between Mg-Mg, Mg-Al, and Al-Al in the three phases indicate a transition from an ordered crystalline structure to a more energetic disordered structure. These behaviors vary among the phases. To characterize the phase structures, a common neighbor analysis was employed. It was found that in the β-Al3Mg2 phase, the Al-Mg atoms are arranged within face-centered cubic (fcc), hexagonal close-packed (hcp), icosahedral (ico), and structure of type other. The ε-Al30Mg23 phase is primarily arranged in icosahedral and other unspecified structures. Meanwhile, the γ-Al12Mg17 phase is arranged in body-centered cubic (bcc), icosahedral, and structure of type other.