In this study, we investigate the intensity and spectral fluctuations in surface-enhanced Raman scattering (SERS) signals from individual plasmonic nanocavities. Extremely long-duration blinking components lasting up to minutes are observed in the SERS intensity fluctuation at room temperature, which can be characterized by successive and random appearance and eventual disappearance of multiple vibrational modes at different frequencies. Theoretical simulations show that multiple hotspots acting on different molecular sites are required to explain these multipeak features, suggesting that the source of long-duration blinking events is multiple single atomic protrusions interacting simultaneously with different sites of individual molecule or each with a different molecule.