Many diseases ordinarily have several kinds of biomarkers (most of them belong to the glycoprotein family). Simultaneous capturing of multiple target glycoprotein biomarkers can obtain better specificity compared with single marker detection in early screening of many diseases. In this work, we attempted to prepare magnetic molecularly imprinted nanoparticles with multiple recognition sites. Horseradish peroxidase and ovalbumin as the frequently used glycoproteins for simulation of glycoprotein biomarkers were employed as dual-templates. The simultaneous preorganization of two templates was achieved by introducing 4-formylphenylboronic acid as a functional monomer. To gain a high adsorption capacity for the two templates, the mass ratio of the two templates was precisely investigated. Controllable polymerization of dopamine was applied to synthesize thin imprinted layers that reduce mass transfer resistance and improve the eluted efficiency of the two templates. The resultant magnetic molecularly imprinted nanoparticles exhibited high adsorption capacities of 34.09 and 51.18 mg g⁻¹, respectively. The simultaneous recognition of two templates in spiked fetal bovine serum was also achieved with satisfactory selectivity. The results indicate that this proposed strategy is potentially applicable for simultaneously and selectively capturing several glycoprotein biomarkers used in detecting many diseases.