A novel magnetic nanoadsorbent (CMCD-APTS-MNPs) containing the superparamagnetic and molecular recognition properties was synthesized by grafting carboxymethyl-β-cyclodextrin (CM-β-CD) on 3-aminopropyltriethoxysile (APTS) modified Fe(3)O(4) nanoparticles. The feasibility of using CMCD-APTS-MNPs as magnetic nanoadsorbent for selective adsorption of adenosine (A) and guanosine (G) based on inclusion and molecular recognition was demonstrated. The as-synthesized magnetic nanoparticles were characterized by TEM, FTIR and TGA analyses. The effects of pH and initial nucleoside concentrations on the adsorption behavior were studied. The complexation of CMCD-APTS-MNPs with both nucleosides was found to follow the Langmuir adsorption isotherm. The CMCD-APTS-MNPs showed a higher adsorption ability and selectivity for G than A under identical experimental conditions, which results from the ability of selective binding and recognition of the immobilized CM-β-CD towards G. The driving force of the separation between G and A is through the different weak interaction with grafted CM-β-CD, i.e., hydrogen bond interaction, which is evidenced by different inclusion equilibrium constants and FTIR analyses of inclusion complexes between grafted cyclodextrin and the guest molecules. Our results indicated that this nanoadsorbent would be a promising tool for easy, fast and selective separation, analysis of nucleosides and nucleotides in biological samples.