Photoisomerization is an important reaction that confers photoresponsive functionality on nanoparticles. Although photoisomerization of molecules forming self-assembled monolayers on two-dimensional surfaces or three-dimensional clusters has been studied, a detailed picture of interactions of molecules undergoing isomerization with nanoparticles is not available. In this paper, we report on the photoisomerization of azobenzene derivatives spatially confined in gold nanoparticle (AuNP) aggregates. AuNP aggregates allow us to simultaneously probe the structural changes of molecules viasurface-enhanced Raman spectroscopy (SERS) and the accompanying changes in interparticle interactions via surface plasmon couplings. AuNP aggregates are formed by the adsorption of synthesized azobenzene-derivatized sulfides (Az) onto the surfaces of AuNPs. The photoisomerization of the adsorbed Az from trans to cis by excitation at 365 nm causes the AuNPs to move close to each other in the aggregates, leading to a redshift of the surface plasmon coupling band in the UV-vis spectra and a concomitant rise in SERS intensity. SERS spectra reveal that the vibrational modes containing the NN stretching character redshift upon irradiation, suggesting that the NN bond is significantly weakened when Az is in the cis form in the AuNP aggregates. The weakening of the NN bond is attributed to the interaction of the NN bond, which is more exposed to the outside in the cis conformation, with the nearby AuNPs that have come closer by the isomerization of adsorbed Az. We find that backisomerization from cis to trans occurs much faster in the AuNP aggregates (k = 1.9 × 10⁻² min⁻¹) than in solution (k = 1.3 × 10⁻³ min⁻¹) because of the reduced NN bond order of cis-Az in the aggregates.