The essence of the chemical mechanism for surface-enhanced resonance Raman scattering (SERRS) is the charge transfer (CT) between the metal and the molecule at the resonant electronic transition, which results in the mode-selective enhancement in the SERRS spectrum. The site-orientated CT can directly interpret the mode-selective chemical enhancement in SERRS. However, it is a great challenge to intutively visualize the orientation and site of the CT. In this paper, for the pyrazine–Au2 complex, a three-dimensional (3D) cubic representation is built to provide direct visual evidence for chemical mechanisms of SERRS via CT from the Au2 cluster to pyrazine at the resonant electronic transition. The relationship between the mode-selective enhancements in SERRS and the site-orientated CT was clearly revealed. The intracluster excitation (analog of plasmon excitation in large naonoparticles) was also visualized by the 3D cubic presentation, which provided the direct evidence of local electromagnetic field enhancement of SERRS. To study the quantum size effect and the coupling effect of the nanoparticles, the photoexcitation mechanisms of the Au20–pyrazine complex and the Au20–pyrazine–Au20 junction were also investigated. The tunneling charge transfer from one Au20 cluster to another Au20 cluster outside the pyrazine in Au20–pyrazine–Au20 junction was also revealed visually. The calculated normalized extinction spectra of Au nanoparticles using the generalized Mie theory reveal that the resonance peak is red-shifted due to the coupling between particles. Copyright © 2009 John Wiley & Sons, Ltd.