Supramolecular chaotropic effect is a new topic in the field of nanocomposites (NCs) fabrication. Herein, this strategy was applied to prepare magnetic Fe3O4@γ‐CD‐boron cluster (SSAs)@Pd NCs in situ via a facile two‐step process, involving a supramolecular assembly process on Fe3O4 NPs and in situ formation of Pd nanoparticles. Boron clusters ([closo‐B12H12]2−) played a dual role in this synthetic process, and were used as a superchaotropic anion to interact with γ‐CD to form supramolecular self‐assemblies (SSAs), as well as efficient reductant to in situ reduce Pd(II) to Pd(0). Ascribed to the electrostatic attraction of boron clusters and capping effect of γ‐CD, ultrafine Pd nanoparticles were successfully coated on the Fe3O4@SSAs composites to fabricate Fe3O4@SSAs@Pd NCs. A combination of UV spectra, Fourier transform infrared spectroscopy, X‐ray photoelectron spectroscopy, transmission electron microscopy, X‐ray diffraction, and energy dispersive X‐ray spectroscopy was used to verify the formation of these magnetic Pd NCs. The ultrafine metallic Pd NPs imparted the magnetic composites with great potential in catalysis, especially for Suzuki coupling reactions. Remarkably, the obtained Fe3O4@SSAs@Pd NCs showed good catalytic performance, high stability and easy recycling via an external magnet.