Abstract: The by-product thenardite (sodium sulfate), generated during wet flue gas desulfurization, poses significant environmental and land-use challenges due to its inherent chemical properties and low resource recovery efficiency. This study addresses this issue by developing a novel approach that leverages modified ion exchange membranes in the electrodialysis process to optimize the separation efficiency of sulfate and sodium ions, facilitating the resource utilization of thenardite. Cation exchange membranes were enhanced through modification with pyrrole and tetraethyl orthosilicate to improve their mechanical strength and sodium ion migration. Anion exchange membranes were treated with polyethyleneimine and dopamine to optimize their surface structure and increase selective permeability for sulfate ions. Characterization techniques, including Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM), revealed that the modified membranes exhibited a significantly enhanced surface negative charge, a more uniform pore distribution, and improved structural compactness. Contact angle measurements indicated that these modifications increased membrane hydrophilicity, thereby increasing ion migration efficiency. Experimental results demonstrated that sodium ion permeability increased by 0.36% for pyrrole-modified cation exchange membranes compared to unmodified membranes, while dopamine-modified anion exchange membranes achieved a 12.57% improvement in sulfate ion permeability. Further electrodialysis experiments showed that, under an applied voltage of 50 V at room temperature, the combination of modified membranes enabled efficient separation of sulfate and sodium ions, achieving a purity of 99%. Notably, after six testing cycles, the modified membranes exhibited excellent stability in ion selectivity and migration efficiency, meeting the requirements for long-term industrial operation. This study innovatively integrates multiple modification strategies to optimize ion exchange membranes, significantly enhancing the separation efficiency and operational stability of the electrodialysis process for thenardite resource utilization. The findings provide crucial technical support for the green resource recovery of thenardite and offer a reference for the treatment of complex industrial wastewater.