We investigated the configuration characteristic and adsorption behavior of 4,4'-thiobisbenzenethiol (TBBT) on the surface of silver nanoparticles (NPs). Under different conditions and preparation processes, several possible surface species were produced including single-end adsorption on a silicon wafer, double-end adsorption and bridge-like adsorption. Although consisting of the same molecule and nano material, different adsorption systems exhibited different spectral characteristics in the surface-enhanced Raman spectroscopy (SERS). A density functional theory (DFT) study further verified the corresponding adsorption states. The combined SERS-DFT study provided a framework towards investigating and designing adsorption systems at a molecular level, indicating the potential use in applications such as nano-sensors.