Magnetic molecularly imprinted polymers (MMIPs) were used to detect and bioseparation of insulin. Because of the significant role of electrostatic interactions, the effects of hydrophilic/hydrophobic interactions were investigated in non-covalent molecular imprinting. The imprinting polymer was synthesized using different type and molar ratios of functional monomers containing acrylamide (AAm) as the neutral-hydrophilic monomer alongside methacrylic acid (MAA) and 2-dimethyl aminoethyl methacrylate (DMA) in the two cases: hydrophilic-hydrophobic-neutral (MMIP3) and hydrophobic-neutral (MMIP2), respectively. The MMIPs adsorption results showed high capacity, good selectivity, and high rapidness to insulin adsorption in both cases. The maximum adsorption (Q) and imprinting factor (IF) of MMIP2 and MMIP3 obtained 54 mg.g−1 and 4.4, and 67 mg.g−1 and 3.2, respectively. In addition, dynamic light scattering results revealed that the average particle size of the surface-modified magnetic nanoparticles (Fe3O4@SiO2@MPS), MMIP2, and MMIP3 were equal to 135 ± 8, 360 ± 21, and 275 ± 28 nm, respectively. The thermogravimetric analysis demonstrated that MNIP2 has almost 25% more polymer layer than MNIP3. VSM analysis was also carried out showed the magnetic power of 21.88, 7.74, and 19.93 emu/g for MNPs, MMIP2, and MMIP3, respectively.