A novel cobalt ion-imprinted polymer (Co(II)-MIIP) based on magnetic Fe3O4 nanoparticles was prepared by using Co(II) as the template ion, and bis(2-methacryloxyethyl) phosphate and glycylglycine as dual functional monomers. The fabricated material was analyzed by Fourier transform infrared spectroscopy, thermogravimetric analysis, field emission scanning electron microscopy, energy dispersive X-ray spectroscopy, Brunauer–Emmett–Teller, X-ray diffraction, and vibrating sample magnetometer. The adsorption experiments with Co(II)-MIIP, found that the maximum adsorption capacity could reach 33.4 mg·g−1, while that of the non-imprinted polymer (Co(II)-NIP) was found to reach 15.7 mg·g−1. The adsorption equilibriums of Co(II)-MIIP and Co(II)-NIP was established within 20 min and 30 min, respectively. The adsorption process could be suitably described by the Langmuir isotherm model and the pseudo-second-order kinetics model. In binary mixtures of Co(II)/Fe(II), Co(II)/Cu(II), Co(II)/Mg(II), Co(II)/Zn(II), and Co(II)/Ni(II), the relative selectivity coefficients of Co(II)-MIIP toward Co(II)-NIP were 5.25, 4.05, 6.06, 11.81, and 4.48, respectively. The regeneration experiments indicated that through six adsorption–desorption cycles, the adsorption capacity of Co(II)-MIIP remained nearly 90%.