In this paper, a detection of trace Hg(Ⅱ) was based on silver nanorods by surface-enhanced Raman spectroscopy (SERS)activity. It was discussed the probe types, which explored that the L-cysteine with a high selectivity and sensitivity for Hg(Ⅱ). The UV/Vis spectra was used to characterize the silver nanorods and its modified the L-Cys. Based on L-cysteine of SERS was high sensitivity and selectivity for Hg(Ⅱ) on condition that the ten kinds of metal ions carried on, but only when the single-peak at 1 040 cm-1 structure appeared after adding the Hg(Ⅱ). SERS sensor with L-cysteine assembled silver nanorods firmly captured the Hg(Ⅱ) through the S-Hg bond. It was valuable to get the molecular probe of the concentration, pH and temperature, in which the result showed the optimization when the density of L-cysteine was 1×10-3 mol·L-1 and pH was 7. It did not have a great effect on temperatures, but was down trend over 55 ℃. In order to protect the structure of L-Cysteine and form complexes rapidly, it was selected temperature about 45 ℃. Under the optimized conditions, a series of the concentration of mercury ions were measured, in which the result showed that the density of mercury ions between 0.01 and 5 μmol·L-1 can be analyzed because of a strong peak at 1 040 cm-1 with good linear relationships (correlation=0.990) with the detection limit of 1 nmol·L-1. Which had very excellent sensitivity and stability. When Hg2+ was tested in real water samples, the recovery was from 85%～103%. It establishes a good way to determine the trace Hg(Ⅱ).