Hierarchical carbon-encapsulated iron nanoparticles (Fe@Cs) with typical core/shell structure are successfully synthesized from starch and iron nitrate by an easy-to-handle process at different carbonization temperatures (600–1000 °C). The nanoparticles are characterized by transmission electron microscopy (TEM), X-ray diffraction (XRD), nitrogen adsorption, and Fourier transform infrared spectroscopy (FTIR). The results show that the carbonization temperature has an important effect on the morphology, the core shape, the diameters, and the porous structure as well as performance of Fe@Cs. Fe@C samples carbonized at 900 °C (Fe@C-900) show the relatively perfect quasi-spherical bcc-Fe core/carbon shell porous structure and their diameters are in a narrow range of 20–50 nm. The adsorption capabilities of Fe@C samples obtained at different carbonization temperatures for removal of thiophene from model oils are evaluated and compared in a batch-type adsorption system. It has been found that among all of the samples measured, Fe@C-900 shows the highest adsorption capability with an increase of 54% for thiophene in comparison with that of the commercial activated carbon. The feasibility of the as-prepared Fe@C-900 as a magnetically separable adsorbent is also demonstrated.