The invention relates to the field of environment monitoring and discloses a silicon-based SERS chip for quantitatively detecting lead ion concentration in an actual water sample and a preparation method thereof. The chip is composed of: a silicon wafer modified with silver nano particles, gold nano particles, nucleotide sequences represented as the SEQ ID No.1, 2, and 4, and a sequence fragment formed by coupling a sulfydryl group to a 5-terminal and coupling a fluorescent dye to a 3-terminal of a nucleotide sequence SEQ ID No.3. In the invention, the surface enhanced Raman scattering silicon-based chip with assistance of polyadenine is employed for detecting the lead ion, wherein the chip is composed of core (silver) and satellite (gold) nano particles, wherein the DNAzyme covalently connected to the chip can be excited specifically by the lead ions, so that the substrate strand is broken into two free DNA segments. The chip can detect a strong SERS signal, and achieves high sensitivity, specificity, repeatability and recyclability.