The development of high-performance electrodes is crucial for advancing capacitive deionization (CDI), a promising technology for energy-efficient water desalination. Among them, Prussian blue analogues (PBAs) with an open framework and high theoretical capacity have shown significant potential as Faradaic electrodes. However, their practical application is limited by poor electron transport and particle aggregation. Herein, we developed an in-situ co-precipitation strategy under acid regulation, where the controlled acidic environment modulates metal ion release and suppresses rapid crystallization, enabling the uniform deposition of small-sized Ni/Co-PBA nanoparticles onto a conductive hollow carbon tube (HCT) support, derived from the Co/Ni salt-melamine co-pyrolysis. The resulting Ni/Co-PBA/HCT composite exhibits significantly enhanced electron transfer kinetics and increased electroactive sites, achieving a high specific capacitance of 344.68 F g−1 at 1 A g−1. When employed as a CDI electrode, it delivers a superior salt adsorption capacity of 73.48 mg g−1 and a remarkable desalination rate of 3.67 mg g−1 min−1 in 1000 mg L−1 NaCl solution at 1.2 V. This study demonstrates the crucial role of transition metal selection in PBA-based electrodes and provides new insights into the rational design of dual-metal materials for efficient water desalination.