Silicon nanoparticles (SiNPs) are biologically compatible, metal-free quantum dots that exhibit size and surface tailorable photoluminescence. The nanostructure of these materials influences their optical, chemical, and material properties and hence plays an important role in their futuregeneration applications in sensors, battery electrodes, optical materials, and contrast agents, among others. In this work, we employ a complement of methods including X-ray photoelectron spectroscopy (XPS), bright-field transmission electron microscopy (TEM), powder X-ray diffraction (XRD), Fourier transform infrared spectroscopy, and 29 Si solid-state nuclear magnetic resonance (NMR) spectroscopy to interrogate the bulk structure of hydride-terminated SiNPs (H-SiNPs) ranging from 3 to 64 nm in diameter and effectively probe their surface. By applying these methods, we have demonstrated that H-SiNPs consist of a size dependent layered structure made up of surface, subsurface, and core silicon regimes. The surface silicon species are manifested by a broad underlying feature in the corresponding 29 Si NMR spectra between −80 to −120 ppm for small nanoparticles (NPs), whereas the sharp resonance at higher frequency (ca. −80.9 ppm, 1 ppm full-width at half-maximum) present in large NPs is attributed to a well-ordered crystalline silicon core. A critical size junction has been identified for 9 nm H-SiNPs, where XPS and NMR show features arising from surface, subsurface, and core silicon species features arising from surface, subsurface, and core silicon species. This structural insight provides essential understanding and potential advancement in the development of SiNP-based applications in photovoltaics, battery anodes, and sensors.