In this work, a novel drug delivery system was developed for thymol. Thymol is an herbal medicine that has low chemical reactivity. The drug delivery platform was Janus Magnetic Nanoparticle. The carrier's core‐shell structure was Fe3O4 nanoparticles (Fe3O4) as core and thin layer SiO2 (SiN) as a shell. The Fe3O4 nanoparticles were synthesized using the co‐precipitation method. A thin layer of SiO2 was covered on the surface of Fe3O4 nanoparticles. The whole Janus magnetic nanoparticle, Fe3O4@SiN, was functionalized with beta‐cyclodextrin (β‐CD) and used as a drug delivery platform. The binding between thymol and the Fe3O4@SiN/β‐CD was made possible through bipolar‐bipolar and hydrogen bonding. The structure, magnetic behavior, and applicability of Fe3O4@SiN for drug delivery purposes were investigated by scanning electron microscopy, X‐ray diffraction spectroscopy, Fourier‐transform infrared spectroscopy, UV–Vis spectroscopy, vibrating sample magnetometer, and energy‐dispersive X‐ray spectroscopy. Vibrating sample magnetometer (VSM) indicated that the Fe3O4@SiN has a weak ferromagnetic behavior (Hc = 65.748G) at temperature 300 K and a permeability of 35.759 × 10−3 emu gG−1. The scanning electron microscopy (SEM) images showed that the particle size of Fe3O4@SiN is 40 nm. Finally, the Fe3O4@SiN/β‐CD was successfully applied to simulated body fluid.