In this paper, BSA surface‐imprinted magnetic Fe‐Ni bimetallic oxide shell nanorods (m‐FeNi@MIPs@PCBMA) were prepared with the assistance of poly(3‐[[2‐(methacryloyloxy)ethyl]dimethylammonium] propionate (PCBMA) in connection with the surface‐imprinting technique. The Fe‐Ni bimetallic oxide shell layer nanorods (m‐FeNi) with magnetic responsiveness simplified the separation and recovery process of adsorbed materials. The controlled introduction of PCBMA facilitated the reduction of protein non‐specific adsorption. At the optimal encapsulation ratio of 1:0.75 (Wm‐FeNi@MIPs: WCBMA), m‐FeNi@MIPs@PCBMA could adsorb 122.98 ± 5.00 mg/g of BSA within 80 min, and the value of the imprinting factor (IF) was also increased from 1.68 (m‐FeNi@MIPs) to 3.95. In the mixed protein adsorption and real sample separation experiments, m‐FeNi@MIPs@PCBMA could selectively separate BSA. Meanwhile, after seven adsorption–desorption experiments, the loss of BSA adsorption by the imprinted nanorods was only 15.9%, which had good reusability. Therefore, m‐FeNi@MIPs@PCBMA has a broader application prospect in the field of protein separation and purification.