Adsorption and chemical enhancement of p-methylbenzenethiol (PMBT) on silver and gold nanoparticle surfaces have been studied using surface enhanced Raman spectroscopy (SERS) and density functional theory (DFT) calculations. In normal Raman spectra, the Raman intensity of the molecule is sensitive to methyl substitution at the para position. DFT calculations for the Raman spectrum of PMBT reproduces well the Raman spectrum in nonpolar solution relative to PMBT in powder. This accords with the order of the PMBT molecules in the solid. The SERS results of PMBT adsorbed on Au and Ag nanoparticles indicate that the Raman intensity in the low-wavenumber region increases with increasing excitation wavelength. The electronic structures of low-lying excited states have been explored for this increase in different PMBT-S-metal cluster complexes. DFT results indicate that low-energy excited states are in fact present and originate from two types of excitations, one localized at the sulfur–silver/gold bonding region and another one from a charge transfer state excited from PMBT to the silver and gold surfaces. Both interfacial excited states contribute significantly to the chemical enhancement mechanism and change relative Raman intensities of adsorbed PMBT. The chemical bonding interaction and the interfacial energy level alignment are therefore important to understand SERS processes of PMBT adsorbed on noble metal surfaces of nanostructures.