Molybdenum disulfide (MoS2) could be a promising electrode candidate for capacitive deionization (CDI) process benefited from the high specific area, excellent electronic conductivity, sound electrochemical stability, and good regenerability. In this work, a CDI study was performed on the desalination performance of water with defect-rich MoS2 sheets as the electrode, in which the defects were fabricated through thermal treatment. The MoS2 with abundant defects on the surface exhibited a much higher desalination capacity than that without any surface modification. The enhancement could be attributed to the abundant negative charges, high specific capacitance and low inner resistance of the defect-rich MoS2, which promoted the electrostatic attraction and electrosorption of Na+ to the electrode surfaces, as well as the formation of a thick electric double layer in the CDI process. The results suggested that defects can be incorporated on the surface of MoS2 for being a superb CDI electrode.