A capacitive deionization system utilizing a pulsed power supply was designed and investigated for desalination. In most studies on capacitive deionization, direct current power supply is the most common power source. Compared with traditional direct-current capacitive deionization, pulsed-capacitive deionization exhibits some excellent properties in desalination: lower power consumption, higher removal rate. The optimal operational conditions of a pulsed power supply in capacitive deionization were discussed in this study. From the experiment results, as for NO 3 of initial concentration 40 mg/L, a duty cycle of 50% and a frequency of 1000 Hz were optimal. From the theory of electrolyte solution, the optimal frequency is related to properties of ion, such as: ionic radius, valence, ion mobility, and also related to the concentration of ion. The results of molecular dynamics simulation were consistent with the experimental results. the reasons for excellent performances of pulsed-capacitive deionization in desalination may be that: the effect of concentration polarization and the migration resistance from solution to the EDL were reduced. Pulsed-capacitive deionization could be used for low concentration water desalination and it provides a new idea for the preparation of ultra pure water and the advanced treatment of wastewater.