A subnanometer gap-separated linear chain gold nanoparticle (AuNP) silica nanotube peapod (SNTP) was fabricated by self-assembly. The geometrical configurations of the AuNPs inside the SNTPs were managed in order to pose either a single-line or a double-line nanostructure by controlling the diameters of the AuNPs and the orifice in the silica nanotubes (SNTs). The AuNPs were internalized and self-assembled linearly inside the SNTs by capillary force using a repeated wet-dry process on a rocking plate. Transmission electron microscopy (TEM) images clearly indicated that numerous nanogap junctions with sub-1-nm distances were formed among AuNPs inside SNTs. Finite-dimension time domain (FDTD) calculations were performed to estimate the electric field enhancements. Polarization-dependent surface-enhanced Raman scattering (SERS) spectra of bifunctional aromatic linker p-mercaptobenzoic acid (p-MBA)-coated AuNP-embedded SNTs supported the linearly aligned nanogaps. We could demonstrate a silica wall-protected nanopeapod sensor with single nanotube sensitivity. SNTPs have potential application to intracellular pH sensors after endocytosis in mammalian cells for practical purposes. The TEM images indicated that the nanogaps were preserved inside the cellular constituents. SNTPs exhibited superior quality SERS spectra in vivo due to well-sustained nanogap junctions inside the SNTs, when compared to simply using AuNPs without any silica encapsulation. By using these SNTPs, a robust intracellular optical pH sensor could be developed with the advantage of the sustained nanogaps, due to silica wall-protection.