The selective recognition, isolation, and subsequent enrichment of target glycoproteins are becoming more and more important in clinical diagnosis. In this work, nano-sized molecularly imprinted polymers integrated double affinity (i.e. metal ion affinity and boronate affinity) (D-MIPs) were prepared for specific separation of ovalbumin (OVA). Poly(styrene-glycidyl methacrylate) nanoparticles (PSG) with epoxy bonds were firstly grafted with iminodiacetic acid (IDA) by ring-opening reaction, and then the Cu2+ was chelated to prepare PSG/IDA-Cu2+. Subsequently, imprinted OVA molecules were pre-immobilized through Cu2+ ion affinity. Finally, a surface imprinting layer was formed though the gentle self-oxidization of a kind of boronic acid ligand (i.e. 3-aminophenylboronic acid, APBA). By washing out imprinted molecules, as-prepared D-MIPs posed higher monolayer binding capacity (138.92 mg g(-1)) and faster capture kinetics (30 min) for OVA, when compared with single affinity integrated MIPs (S-MIPs) and non-imprinted polymers (NIPs), and the chemical adsorption dominated double affinity was the rate-determining step for whole adsorption process. The imprinting factor (IF) of OVA, horseradish peroxidase (HRP) and bovine serum albumin (BSA) by the available D-MIPs were 4.44, 2.23 and 1.47, respectively, which confirmed the better selectivity for OVA. D-MIPs performed favorable regeneration ability and a promising application in actual sample. In addition, a combination of synergistic multiple bindings and imprinting effect, as the mechanism for enhancing specific separation, was also demonstrated.