In order to improve dispersibility, polymerization characteristics, chemical stability, and magnetic flocculation performance, magnetic Fe3O4 is often assembled with multifarious polymers to realize a functionalization process. Herein, a typical three-dimensional configuration of hyperbranched amino acid polymer (HAAP) was employed to assemble it with Fe3O4, in which we obtained three-dimensional hyperbranched magnetic amino acid composites (Fe3O4@HAAP). The characterization of the Fe3O4@HAAP composites was analyzed, for instance, their size, morphology, structure, configuration, chemical composition, charged characteristics, and magnetic properties. The magnetic flocculation of kaolin suspensions was conducted under different Fe3O4@HAAP dosages, pHs, and kaolin concentrations. The embedded assembly of HAAP with Fe3O4 was constructed by the N-O bond according to an X-ray photoelectron energy spectrum (XPS) analysis. The characteristic peaks of -OH (3420 cm-1), C=O (1728 cm-1), Fe-O (563 cm-1), and N-H (1622 cm-1) were observed in the Fourier transform infrared spectrometer (FTIR) spectra of Fe3O4@HAAP successfully. In a field emission scanning electron microscope (FE-SEM) observation, Fe3O4@HAAP exhibited a lotus-leaf-like morphological structure. A vibrating sample magnetometer (VSM) showed that Fe3O4@HAAP had a relatively low magnetization (Ms) and magnetic induction (Mr); nevertheless, the ferromagnetic Fe3O4@HAAP could also quickly respond to an external magnetic field. The isoelectric point of Fe3O4@HAAP was at 8.5. Fe3O4@HAAP could not only achieve a 98.5% removal efficiency of kaolin suspensions, but could also overcome the obstacles induced by high-concentration suspensions (4500 NTU), high pHs, and low fields. The results showed that the magnetic flocculation of kaolin with Fe3O4@HAAP was a rapid process with a 91.96% removal efficiency at 0.25 h. In an interaction energy analysis, both the UDLVO and UEDLVO showed electrostatic repulsion between the kaolin particles in the condition of a flocculation distance of <30 nm, and this changed to electrostatic attraction when the separation distance was >30 nm. As Fe3O4@ HAAP was employed, kaolin particles could cross the energy barrier more easily; thus, the fine flocs and particles were destabilized and aggregated further. Rapid magnetic separation was realized under the action of an external magnetic field.