To date, saline eluent from the ion exchange process in the extraction of traditional Chinese medicine such as Leonurus japonicus Houtt was treated predominantly by the conventional processes such as evaporation, crystallization and ethanol elution. However, large amount of energy and fresh organic solvent need to be consumed in the above processes. In the present study, two-stage electrodialysis (ED) was proposed to simultaneously recover salt and purify zwitterionic stachydrine from the saline eluent. In the first stage ED, the membrane type and current density were optimized, and then the continuous twenty-batch operation in partial cyclic mode was carried out to increase the concentration of the recovered NaCl solution. Subsequently, the second stage ED was carried out to further purify the above desalinated saline eluent. Results indicate that, after the two-stage ED process, the concentrated NaCl solution can be directly recycled due to the high concentration of 2.9 mol/L; the recovery rate and purity of NaCl can reach to high values of 99.8% and 99.6%, respectively; the recovery rate and purity of stachydrine can reach to high values of 95.6% and 99.3%, respectively. In addition, a low energy consumption (∼8.34 kWh/m3) was required for the two-stage ED system. What's more, the membrane fouling investigation indicated that there are as little as 0.5% of the total stachydrine in the saline eluent adsorbed into the CEM. Nonetheless, ED process can be operated stably due to the relatively stable membrane resistance and cell pair voltage drop. Hence, the two-stage ED system is a high-efficient, environmentally-friendly and economical process for simultaneous salt recovery and zwitterionic stachydrine purification from the saline eluent.