To overcome the drawback of carbon nanofibers (CNFs) such as the low energy density and low specific capacitance as electrode for supercapacitors, SiO2/PANI@CNFs composite was prepared by layer-by-layer (LbL) assembly technique, in which the SiO2 served as a component for improving capacitive behavior. Polyaniline (PANI) is used as nucleation site for synthesizing SiO2 particles as well as active material for improving capacitance. In this study, SiO2 particles were synthesized using biosilicification process as a bioinspired, rapid, and facile synthetic route for SiO2 particles at ambient temperature and pressure, etc. To elucidate effect of SiO2 on the electrochemical properties, SiO2/PANI@CNFs samples were prepared by varying concentration ratio of tetraethyl orthosilicate (TEOS) to CNFs. It was observed that the specific surface area and the capacitance are highly dependent on the TEOS concentration. The capacitance of the composite prepared at the TEOS concentration of 0.19 mmol reaches 412 F g−1 at the current density of 1 A g−1. These results are attributed to increased specific surface area from interstitial voids between SiO2 particles and hydrophilic nature of SiO2 particles, which offers sufficient channels for rapid ion diffusion and leads easy accessibility to the active sites for the electrochemical reaction between electrode and aqueous electrolyte. Due to its excellent electrochemical and biocompatible properties, bioinspired SiO2 inorganic material will promote the development of energy storage devices in biomedical and environmental electronics.