The invention discloses a high-throughput screening technology of a targeted drug, which comprises the following steps: respectively coupling a metal nanoparticle probe or a magnetic bead probe to a Raman signal molecule, a target protein or a target protein binding receptor protein, simultaneously adding the substances into a compound to be screened, incubating, finally detecting a Raman signal, and judging whether the compound to be screened is a targeted inhibitor or not, the targeted inhibitor having the characteristic of inhibiting target protein related biological activity. Raman signal detection is applied to the technical field of targeted new drug screening for the first time, and metal nanoparticles and magnetic beads are combined to form a simple and sensitive new drug screening method. Meanwhile, the method is small in measurement interference, small in required sample amount, strong in signal, high in sensitivity and easy and convenient to operate, cleaning is not needed in the whole detection process, and a new strategy is provided for a targeted drug screening approach.