In the present article, normal Raman spectra (NRS) and surface-enhanced Raman spectra (SERS) of L-cysteine (L-Cys) included liquid and solid sample, the unique possessing the reducing group, on the silver nanorodes were analyzed. The results showed that the strengthen of peaks were enhanced relatively. The vibrational and enhanced peaks were assigned. Adsorption models of L-Cys on the silver nanorodes have been investigated. The S—H stretching vibration absorption of solid NRS was found, which was disappeared on the SERS, which showed that the ν(S—H) bond was formed by drawing lone pairs of electrons on the sulfur atoms and silver nanorodes. The vibrations of ν(C—O) and ν(C—N) was enhanced obviously. The results explain that the long pair electrons of L-Cys were adsorbed on the silver nanorodes with moving to the low wave numbers. At the different pH values, all the different shifts were expressed and adsorption behaviors were changed. When the pH values reached number of 6, the vibrations of ν(S—H) were disappeared, it is shown that it was formed the stable vibrations of ν(Ag—S). With the pH values tended an alkalinity, but carboxyl groups were enhanced because of connection with silver nanoeodes. Under the condition of pH values 7, vibrations of ν(Ag—S) were constituted meanwhile had the stable vibrations of ν(C—O) and ν(C—N), so it was selected the pH values 7. In the systems containing different metal salts including Na+, Mg+, Cu2+, etc, it was found that the molecular structure of the L-Cys was changed under adding metal salts with Al3+, Cu2+, Zn2+, Cd2+ and Hg2+, the ability depends on metal ions and carboxyl groups were conjugated. UV-Vis absorption of silver nanorods was observed at 414nm, when it was changed under adding the metal salts. But the maximum absorption peaks were small changed, which had not assembled. Cu2+, Zn2+, Cd2+ and Hg2+ were all created that the groups ν(C—S) was appeared the two weak peaks near for 661 cm-1. The Al3+ came into precipitation with carboxyl groups easily, so the SERS was the weakest to low resolution. With the radius of metals (Cu2+, Zn2+, Cd2+, Hg2+) grow, the interaction was enhanced with sulfur atom. The Cd2+ and Hg2+ belonged to soft acid and S2- to soft base, so both were had large force. The SERS of complexes of cupric ion because of unstable (n-1)d9 electron configurations with L-Cys were reduced because of precipitation combining cupric ion with sulfhydryl groups to obtain the insoluble thiolate salts. The SERS of complexes of mercury ion with L-Cys only appeared the vibrations of ν(C—O), without any other vibration. The structure of L-Cys to join the mercury ion was destroyed completely. Though alternating the condition of pH value, proportion and concentration, the SERS of complexes of metal ions with L-Cysteine was changed. The results show that the strengthen of peaks were decreased as the pH value, proportion and concentration increased, which provides important information for the protein denaturation and heavy metal pollution.