Electrodialysis, an efficient and environmental friendly separation technology, plays a significant role in water treatment. In order to reveal ion transfer mechanism and predict electrodialysis behavior, a mathematical model for steady transport of a binary electrolyte during the desalination process was developed. The Nernst–Planck, electroneutrality equations, and other hydrodynamic equations were coupled and solved with appropriate boundary conditions using the finite element method. This model is capable to predict the local ion concentration, electric potential, and ion flux in a rectangular electrodialysis unit. The effects of voltage drop (0.4–1.0 V), inlet velocity (0.03–0.06 m/s), and initial feed concentration (500–700 mol/m3) are investigated, which could provide valuable guidance for electrodialysis operation in the practical project. Moreover, this model is validated by comparing its simulation result with experimental data of electrodialysis, and it could predict the desalination of saline water accurately. Ion transfer modeling provides an effective way to study the transfer mechanism, estimate the effects of various parameters conveniently, and realize the target‐oriented operation optimization.