Studying the distribution and transport dynamics of cations in plants is crucial for understanding their response mechanisms to saline–alkali stress conditions. However, our current understanding of how restoration measures affect cation distribution and transport in plants is surprisingly limited. To address this gap, we conducted a split-plot experiment using Medicago sativa L. cv. “Zhongmu No. 1” to investigate the combined effects of biological and chemical restoration measures—with bio-fertilizer as the primary zone and flue gas desulfurization (FGD) gypsum and with humic acid as the secondary zone—on soil properties, plant growth, and the content, distribution, and transport of cations in plants. The results revealed that bio-fertilizers exhibited positive effects on the plant growth, yield, and translocation of key ionic components to leaves. On the contrary, FGD gypsum with humic acid reduced the soil’s pH level, exchangeable sodium percentage (ESP), and sodium adsorption ratio (SAR) while increasing the contents of K+, Ca2+, and Mg2+ in the soil. The combination of bio-fertilizer, FGD gypsum, and humic acid increased the biomass and enhanced the translocation of Mg2+ to leaves. The distribution and transport of Mg2+ within the plant constituted pivotal elements for enhancing plant growth through restoration strategies. The application of bio-fertilizer, FGD gypsum, and humic acid reduced Na+ transport in M. sativa by enhancing the selective absorption of beneficial ions in leaves and by facilitating the transport of Ca2+ and Mg2+ from stems to the leaves. This, in turn, increases the salt tolerance of plants and promotes their growth. Our results offer new insights into the interactions among measures, soil, and plants in saline–alkali land restoration, providing practical solutions for the restoration of saline–alkali soil.