Pursuing improved electrode materials is essential for addressing the challenges associated with large-scale Li-ion battery applications. Specifically, silicon oxide (SiO) has emerged as a promising alternative to graphite anodes, despite issues related to volume expansion and rapid capacity degradation. In this study, we synthesized carbon-coated SiO using diatom biomass derived from artificially cultured diatoms. However, the inherent carbon content from diatoms poses a significant challenge for the electrochemical performance of diatom-based anodes in large-scale applications. Subsequently, we conducted further research and demonstrated excellent performance with a carbon content of 33 wt.% as anodes. Additionally, real-time characterization of the carbonization process was achieved using thermogravimetry coupled with infrared spectroscopy and gas chromatography mass spectrometry (TG-FTIR-GCMS), revealing the emission of CO and CO during carbonization. Furthermore, electrochemical tests of the processed diatom and carbon (PD@C) anode exhibited outstanding rate capability (~500 mAh g at 2 A g), high initial Coulomb efficiency (76.95%), and a D diffusion rate of 1.03 × 10 cm s. Moreover, structural characterization techniques such as HRTEM-SAED were employed, along with DFT calculations, to demonstrate that the lithium storage process involves not only reversible transport in LiSiO and LiSi, but also physical adsorption between the PD and C layers. Exploring the integration of diatom frustules with the intrinsic carbon content in the fabrication of battery anodes may contribute to a deeper understanding of the mechanisms behind their successful application.