In this study, carbon aerogels (CAs) were synthesized by the sol-gel method, using environmentally friendly glucose as a precursor, and then they were further activated with potassium hydroxide (KOH) to obtain activated carbon aerogels (ACAs). After the activation, the electrochemical performance of the ACAs was significantly improved, and the specific capacitance increased from 19.70 F·g−1 to 111.89 F·g−1. Moreover, the ACAs showed a stronger hydrophilicity with the contact angle of 118.54° compared with CAs (69.31°). When used as an electrode for capacitive deionization (CDI), the ACAs had not only a better diffuse electric double layer behavior, but also a lower charge transfer resistance and intrinsic resistance. Thus, the ACA electrode had a faster CDI desalination rate and a higher desalination capacity. The unit adsorption capacity is three times larger than that of the CA electrode. In the desalination experiment of 100 mg·L−1 sodium chloride (NaCl) solution using a CDI device based on the ACA electrode, the optimal electrode spacing was 2 mm, the voltage was 1.4 V, and the flow rate was 30 mL·min−1. When the NaCl concentration was 500 mg·L−1, the unit adsorption capacity of the ACA electrode reached 26.12 mg·g−1, much higher than that which has been reported in many literatures. The desalination process followed the Langmuir model, and the electro-sorption of the NaCl was a single layer adsorption process. In addition, the ACA electrode exhibited a good regeneration performance and cycle stability.