Abstract: The non-renewability of limestone resources leads to the gradual scarcity of high-quality limestone, and the development of calcium-based desulfurizers with low-grade magnesian limestone as the raw material for the production of calcium-based desulfurizers is of great significance for the control of SO₂ emissions in highly polluting industries. In this study, the desulfurization performance of magnesian hydrated lime under high temperature flue gas conditions and the influence of Mg on Ca(OH)₂ crystal structure were explored by using a fixed-bed desulfurization experimental system combined with XRD characterization technology. The role of Ca(OH)₂ crystal structure in influencing the surface chemical reaction stage and diffusion control stage of the desulfurization reaction is investigated by the kinetic approach using the equivalent particle model, and the key steps governing the magnesian hydrated lime desulfurization reaction are clarified. Based on Density Functional Theory (DFT), the adsorption behavior and sulfidation reaction of SO₂ on clean and Mg-doped Ca(OH)₂ surfaces are investigated, and the diffusion behavior of Ca²⁺ in the two lattice systems is probed. Based on the experimental and simulation calculation results, the Na⁺ additive is used to potentiate the desulfurization performance of magnesian hydrated lime, and the potentiation mechanism is revealed. The results show that Mg²⁺ affects the crystal structure of Ca(OH)₂ in hydrated lime by substituting Ca²⁺, and the change in the crystal structure of Ca(OH)₂ is the main reason for the change in the desulfurization performance of magnesian hydrated lime. The surface oxygen atom is the active site for SO₂ adsorption, and the substitution of Mg²⁺ for Ca²⁺ enhances the adsorption of SO₂ on the surface substrate of Ca(OH)₂, and the sulfation reaction energy barrier decreases from 1.40 eV to 1.11 eV, so that there is a facilitating effect on the surface chemical reaction phase of desulfurization reaction. At the same time, it also enhances the bonding interaction between Ca²⁺ and OH⁻ within the Ca(OH)₂ crystals, and the Ca²⁺ diffusion energy barrier increases from 0.98 eV to 1.55 eV, which is not conducive to the ion diffusion inside the crystal, so it has an inhibitory effect on the diffusion control stage. The lattice distortion of Ca(OH)₂ is maximized at a NaOH addition concentration of 5%, and the sulfur capacity reaches 98.42 mg/g, which is an enhancement of about 42.92%. Na⁺ doping into the lattice of Ca(OH)₂ is able to weaken the bonding cooperation of Ca—O, and the diffusion energy barrier of Ca²⁺ is reduced to 1.26 eV, which can promote the migration of solid ions inside the crystal, and significantly improve the desulfurization performance of magnesian hydrated lime.