Vaterite calcium carbonate (CaCO3) possesses unique advantages compared to calcite; however, some critical issues need to be addressed, such as vaterite stability. Numerous studies have indicated that NH4+ can promote vaterite formation and prevent its transformation. However, as vaterite is an instantaneous microscopic process that is easy to transform, directly revealing the role of NH4+ in stabilizing vaterite remains challenging in experiments. This research aims to reveal the role of NH4+ in stabilizing vaterite and retarding phase transformations. Vaterite stabilization was investigated at different NH4+ concentrations and characterized by XRD and SEM. The reaction system’s pH, electrical conductivity, and surface tension changes were analyzed in the presence of NH4+. Computational and experimental studies were utilized to determine the role of NH4+ in the stabilization of vaterite. Results revealed that NH4+ can significantly increase the existence time of vaterite in the water solution. The density functional theory (DFT) indicated that the adsorption energy of NH4+ and vaterite (110), (112), and (114) is obviously higher than that of H2O molecules. The molecular dynamics (MD) simulation research shows that NH4+ can replace water molecules on the crystalline surface of vaterite and mainly interact with carbonate ions on the surface of vaterite. The mechanism analysis shows that the inhibitory effect of NH4+ on the phase transformation of vaterite is primarily caused by preventing the dissolution process. This study systematically explains the role of NH4+ in the stability of vaterite and further reveals that NH4+ can not only promote the formation of vaterite but also play a decisive role in inhibiting its phase transition.