Raman scattering spectra and optimized geometries of the 1,4-benzenedithiol molecule and complexes have been calculated using density functional theory (DFT) with B3LYP functional at the level of 6-311G+(d) basis set for C,H,S atoms and LanL2DZ for Ag， Au atoms， respectively. The optimized 1,4-benzenedithiol molecule was non-planar structure and the angle between benzene ring plane and S—H is 20. 20. By means of the simulation of molecule adsorbed on gold and silver cluster， we concluded that gold clusters are nearly parallel to the benzenedithiol molecule and silver clusters are almost perpendicular to the molecular surface. The authors studied the interaction between Raman intensity and molecular properties， such as static polarizablity and charge distribution. The Raman intensity of 1,4-BDT-Au2， 1,4-BDT-Ag2 and Ag2-1,4-BDT-Au2 were in good agreement with static polarizability. The excited states of Ag2-1,4-BDT-Au2 complex were calculated using time-dependent density functional theory (TDDFT). And the simulated absorption spectra and several allowed singlet excited states were analyzed to investigate the surface-enhanced Raman chemical enhancement mechanism.