Estimating and increasing limiting current density (LCD) levels is of fundamental importance for the development of electrodialysis (ED) systems, and it is becoming clear that the use of porous spacers can significantly increase such LCD levels. In this study, a three-dimensional numerical simulation was proposed for evaluating the mass transfer within a porous spacer unit cell and for estimating LCD levels. It was found that our proposed method is effective for estimating the minimum value of an LCD, which is a significant factor related to the safe operation of ED systems. Furthermore, it was found that increasing the minimum effective Sherwood number provides a key to increasing LCD levels. Porous spacer design guidelines were proposed based on the numerical simulation results, after which a new spacer was introduced, designed according to those guidelines. It was found that flow disturbances on the membrane caused by porous spacer structures can lead to increases in effective Sherwood numbers and that LCD levels could be increased by eliminating the flow stagnation behind the structures on the membrane. The LCD of our new spacer was found to be higher than that of the spacers with the highest LCD levels in use at present. Therefore, we can conclude that the proposed design guidelines are effective for increasing LCD levels.