In this work, a new technique of polarity-regulating molecular self-assembly was used for fabricating core shell magnetic nanoparticles (NPs) with a high content of carboxy groups. First, Fe3O4 NPs with hydrophobic surfaces were prepared. Then the NPs were dispersed in a medium of water and suspended for the procedure of the molecular self-assembly of 4-vinylbenzoic acid. In this case, the molecules might move towards the surfaces of hydrophobic NPs in manner of carboxy groups outwards. After that, in situ polymerization was initiated and poly(4-vinylbenzoic acid) was formed around the surfaces of Fe3O4 NPs. Core shell magnetic NPs with a high content of carboxy groups were fabricated. The prepared NPs were characterized by Fourier transform infrared (FTER), thermogravimetric analyses (TGA), transmission electron microscopy (TEM), vibrating sample magnetometer (VSM), and conductivity titration.