Prussian blue analogues (PBAs), as the representative of Faradaic materials, has drawn extensive attention in capacitive deionization (CDI) for unique redox activity, open framework structure, and low-cost synthesis. However, the serious aggregation, low conductivity, and easy structural collapse of PBAs nanoparticles limit the practical application in CDI. Herein, the ternary composite Ni,Co-PBA@MXene/PPy is flexibly constructed by integrating the collective advantages of Ni,Co-PBA, MXene, and PPy. In this configuration, MXene not only provides high conductivity but also acts as the good substrate for the in-situ homogeneous growth of Ni,Co-PBA nanoparticles. Furthermore, Ni,Co-PBA nanoparticles could effectively inhibit the self-stacking of MXene and facilitate fast ion intercalation. And the doping of Co in Ni,Co-PBA promotes the redox process by the pseudocapacitive contribution. Meanwhile, PPy contributes to accelerating ions transport rate and promoting the structural stability of MXene and Ni,Co-PBA. Consequently, the hybrid CDI cell AC//Ni,Co-PBA@MXene/PPy delivers prominent desalination performance with the high salt adsorption capacity (38.7 mg g−1), rapid salt adsorption rate (10 mg g−1 min−1), low energy consumption (0.283 kWh kg−1-NaCl), and outstanding cyclic stability. Most importantly, the Ni,Co-PBA@MXene/PPy electrode can reserve favorable structural integrity by the significant shielding effect of PPy to prevent Ni,Co-PBA from collapse and MXene from being oxidized.