The desalting process in a desalting battery involves ion transport in pores, diffusion in active particles and electrochemical reactions at the interface between the solution and active particles. In this paper, the quartet structure generation set (QSGS) was used to generate a two-dimensional porous microstructure. Based on the lattice Boltzmann method, the dynamic process on the pore scale has been studied, revealing the dynamic change process of sodium concentration in the electrode during desalination. The effects of different porous electrode structures (porosity, particle size, and electrode thickness) and operating parameters (initial flow rate and concentration) on the desalination performance were studied. The simulation results show that the diffusion resistance of ions in the active particles with an irregular shape and small size in the porous electrode is low and sodium ions can migrate and embed in the active particles faster, which is beneficial for a rapid desalination process. In a certain range, increasing the electrode porosity, decreasing the electrode thickness and increasing the initial concentration and speed of the solution can shorten the total time of sodium ion embedding in the active particles and speed up the desalination process, and decreasing the electrode thickness has the best effect.