Membrane capacitive deionization (MCDI) has emerged as a promising electric-field-driven technology for brackish water desalination and specific salt or charged ion separation. The use of carbon-based or pseudocapacitive materials alone for MCDI usually suffers from the drawbacks of low desalination capacity and poor cycling stability due to their limited accessible adsorption sites and obstructed charge-carrier diffusion pathways. Therefore, developing a hybrid electrode material with multiple charge storage mechanisms and continuous electron/ion transport pathways that can synergistically improve its specific capacitance and cycling durability has currently become one of the most critical technical demands. Herein, we developed a novel hierarchically architectured hybrid electrode by first spinning MXene into polyacrylonitrile (PAN)-based carbon nanofibers (MCNFs) to obtain a highly conductive carbon nanocomposite framework. The excellent spatial support structure can effectively prevent the dense packing of Cl–- and DBS–-doped polypyrrole (PPy) molecular chains during the following electrodeposition process, which not only ensures the efficient transport of electrons in the continuous hybrid carbon nanofibrous skeleton but also provides abundant accessible sites for ion adsorption and insertion. The obtained self-supporting membrane electrodes (MCNF@PPy+Cl– and MCNF@PPy+DBS–) have the advantages of outstanding specific capacitance (318.4 and 153.9 F/g, respectively), low charge transfer resistance (10.0 and 5.3 Ω, respectively), and excellent cycling performance (78% and 90% capacitance retention ratios, respectively, after 250 electrochemical cycles). Furthermore, the asymmetrical membrane electrodes showed a superior desalination capacity of 91.2 mg g–1 in 500 mg/L NaCl aqueous solution and obvious divalent ion (Ca2+, Mg2+) selective adsorption properties in high-salt water from the cooling towers of thermal power plants.