Surface plasmon resonance (SPR) sensors are based on photon-excited surface charge density oscillations confined at metal-dielectric interfaces, which makes them highly sensitive to biological or chemical molecular bindings to functional metallic surfaces. Metal nanostructures further concentrate surface plasmons into a smaller area than the diffraction limit, thus strengthening photon-sample interactions. However, plasmonic sensors based on intensity detection provide limited resolution with long acquisition time owing to their high vulnerability to environmental and instrumental noises. Here, we demonstrate fast and precise detection of noble gas dynamics at single molecular resolution via frequency-comb-referenced plasmonic phase spectroscopy. The photon-sample interaction was enhanced by a factor of 3,852 than the physical sample thickness owing to plasmon resonance and thermophoresis-assisted optical confinement effects. By utilizing a sharp plasmonic phase slope and a high heterodyne information carrier, a small atomic-density modulation was clearly resolved at 5 Hz with a resolution of 0.06 Ar atoms per nano-hole (in 10–11 RIU) in Allan deviation at 0.2 s; a faster motion up to 200 Hz was clearly resolved. This fast and precise sensing technique can enable the in-depth analysis of fast fluid dynamics with the utmost resolution for a better understanding of biomedical, chemical, and physical events and interactions.