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 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 different restoration strategies decreased soil alkalinity and enhanced plant growth. Significantly, bio-fertilizer exhibited positive effects on plant growth and yield. On the contrary, FGD gypsum with humic acid reduced the soil's pH level, exchangeable sodium percentage, and sodium adsorption ratio, while increasing the contents of K+, Ca2+, and Mg2+ in the soil. The triple combination of FGD gypsum and humic acid with bio-fertilizer reduced Na+ transport in M. sativa by enhancing the selective absorption of beneficial ions, such as K+, Ca2+, and Mg2+ in leaves, and by facilitating the transport of Ca2+ and Mg2+ from roots and stems to the leaves. Therefore, the application of FGD gypsum and humic acid combined with bio-fertilizer has the potential to decrease soil alkalinity and the proportions of water-soluble ions in the soil, ultimately enhancing the translocation of key ionic components to 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.