A cell-based sensor based on surface-enhanced Raman scattering and an application thereof. The cell-based sensor is established by guiding a surface-enhanced Raman scattering probe into a human liver cell line; the surface-enhanced Raman scattering probe is prepared by using a gold nanoparticle as a testing substrate, a gene damage effector molecule antibody as a recognition unit, a Raman molecule as a reporting unit, SH-PEG-NH2 as a stable chain and a cell-penetrating peptide as an auxiliary penetration unit; and the cell-based sensor is exposed to various drug impurities, a Raman signal is detected, and a type and a level of the genotoxic impurities are assessed.