Here, we report our results on excitation intensity and nanoscale Ag cluster dependent spectral fluctuation dynamics of surface enhanced Raman scattering. We have studied single-Ag-cluster surface enhanced Raman scattering (SERS) intensity fluctuations under low molecule surface coverage of rhodamine 6G (R6G) and cytochrome c. By applying both experimental and theoretical approaches, we observed that spectral fluctuation phenomena are associated with SERS not only from single-molecule loaded nanoclusters but also from submonolayer molecule loaded nanoclusters. The nanoscale confinement of the local electric field enhancement under the laser excitation defines the SERS fluctuation. A new AFM-coupled two-channel photon time-stamping system, enabling in situ correlation of the topographic and spectroscopic information for single nanoparticle clusters, was used to record Raman intensity fluctuation trajectories at sub-μs resolution. Experimentally, we found that SERS fluctuation dynamics are highly inhomogeneous amongst nanocluster interstitial sites. Although the fluctuation above ~50 W/cm2 excitation is dominated by photoinduced processes, spontaneous fluctuation can be observed at lower excitation intensity. Although a single Raman-active molecule confined within the volume of an electric field excitation gives a significant Raman spectral fluctuation, observation of the fluctuation alone may not be sufficient in identifying a single-molecule origin of a Raman spectrum. The Raman signal comes predominately from the localized electric field enhancement at interstitial sites, occuring in a very small volume at nanoscale (capable of holding only one or a few molecules), as estimated from finite-element methods simulations of an electric field enhancement using a classical electrodynamics approach. Such a small number of molecules, which are presumably under discrete diffusion and exposed to interactions with a locally strong electric field, results in the observed Raman fluctuation. The fluctuation autocorrelation amplitude is proportional to the reverse number of molecules confined at the volume of the electric field enhancement.