In this work, we report the synthesis of carbon@Na4Ti9O20 (C@NTO) core-shell nanotube as novel electrodes for hybrid capacitive deionization (HCDI) with enhanced performance to overcome the several key issues of desalination. The C@NTO nanotube exhibits a highly improvement in electrochemical performance, i.e. specific capacity, capacitance retention and impendence. As predicted from Langmuir isotherm, the C@NTO based HCDI shows an ultrahigh salt removal capacity of 80.56 mg/g at cell voltage of 1.4 V. Moreover, the charge efficiency of C@NTO is closely approach to 1 even in high concentrated stream. The enhancement in salt removal capacity of the HCDI is attributed to the presence of chemical bond, resulting in insertion-desertion of Na ions into C@NTO during the desalination. Besides, the C@NTO possesses the improved specific surface area and low resistivity as compared to pure NTO, both of which are beneficial to increase the penetration of salty ions and the ion removal rate. These results suggest that the C@NTO core-shell nanotube is a feasible electrode material for desalination in the HCDI process.