Electrodeionization (EDI), as a combination of electrodialysis and mixed-bed ion exchange process, manage to show the separation effectiveness that provides a solution to various modern deionization purposes. In this study, the performance of EDI in seawater desalination is investigated under controlled applied voltage. The variation of applied voltage ranging from 10 to 50 volt is introduced to the EDI system to study its desalination kinetics. At constant feed water TDS, applied voltage, spacer thickness, and system recovery significantly affect final diluate TDS. EDI demonstrate a good performance in seawater desalination with removal efficiency around 98.7%. Initially, diluate TDS decrease with applied voltage but increase again after reach minimum point due to back diffusion and water splitting effect. System recovery shows a negative effect on diluate quality. Two-stage operation can effectively enhance ion transport and minimize back diffusion problem. Long-term performance test suggests that EDI cell with 4 mm spacer is the best system in this experimental area with the lowest diluate TDS. The specific energy consumption of EDI process in seawater desalination is 12.96 kWh/m³ which is lower than SWRO at a small production capacity (less than 3.6 m³/h). This study also recommends low voltage operation to minimize Joule Heating effect.