•A high-performance Prussian blue analog was prepared by controlled nickel–cobalt doping.•Prussian blue's framework offers good sodium storage capacity and cycling stability.•Ni-Co ratio was controlled to prepare PB analogs.•A PB analog with Ni:Co=1:2 ratio showed high desalination capacity and rate.•The obtained PB analog retained 98% of its capacity after 50 cycles. The unique framework structure of Prussian blue imparts excellent sodium storage capacity and cycling stability, thus making it an ideal capacitive deionization (CDI) electrode. Herein, Prussian blue analogs were prepared by the controlled doping of nickel–cobalt bimetallic ions to improve their desalination capacity and stability. Process parameters such as cell potential, current, inlet flow rate, and solution concentration were investigated to determine the optimal conditions for Prussian blue desalination, and a high-performance Prussian blue analog (CNF-4) was successfully synthesized by accurately controlling the nickel–cobalt doping ratio. The desalination capacity and rate of CNF-4 (Ni:Co=1:2) reached 65.31 mg g−1 and 4.38 mg g−1 min−1, respectively, and 98% of the capacity retention rate was maintained after 50 cycles of desalination. The excellent capacity and performance of the CNF-4 material indicate its superiority to conventional PBA CDI electrodes and its prospective applications in seawater desalination.