Near-field enhanced bifunctional plasmonic-magnetic (PM) nanostructures consisting of silica nanotubes with embedded solid nanomagnets and uniformly dual-surface-coated plasmonic Ag nanoparticles (NPs) are rationally synthesized. The solid embedded sections of nanotubes provide single-molecule sensitivity with an enhancement factor up to 7.2 × 109 for surface-enhanced Raman scattering (SERS). More than 2× SERS enhancement is observed from the hollow section compared to the solid section of the same nanotube. The substantial SERS enhancement on the hollow section is attributed to the dual-sided coating of Ag NPs as well as the near-field optical coupling of Ag NPs across the nanotube walls. Experimentation and modeling are carried out to understand the dependence of SERS enhancement on the NP sizes, junctions, and the near field effects. By tuning the aspect ratio of the embedded nanomagnets, the magnetic anisotropy of nanotubes can be readily controlled to be parallel or vertical to the long directions for nano-manipulation. Leveraging the bifunctionality, a nanotube is magnetically maneuvered to a single living mammalian cell amidst many and its membrane composition is analyzed via SERS spectroscopy.