Monodisperse, uniform, and hierarchically mesostructured silica particles with a thin shell have been fabricated via one-step synthesis using dodecanethiol (C-12-SH) and CTAB as dual templates. A series of hierarchically mesostructured silica particles with a morphology similar to that of pomegranate can be obtained by simply adjusting the mass ratio of C-12-SH to CTAB. When the mass ratio is increased, a mesophase transformation occurs from an ordered 2D hexagonal structure to a mesostructured cellular foam in the core of the hierarchically mesoporous silica particles. These unique silica particles are characterized by small-angle X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and energy dispersive spectroscopy (EDS), Fourier transform infrared spectroscopy (FT-IR), and nitrogen adsorption-desorption measurements. The formation mechanism of the hierarchically mesostructured silica particles with a thin shell is proposed according to the experimental results. Synergistic self-assembly of C-12-SH and CTAB in the solution is believed to play a key role in mediating the formation of these hierarchical silica mesostructures, and the hydrophobic dodecanethiol can act as both the swelling agent for CTAB micelles and coagent for the formation of a microemulsion with CTAB micelles. This synthesis method is simple, straightforward, and suitable for the preparation of the other biomineral nanostructures that are unique scaffolds in biological, medical, and catalytic applications.