The invention provides a method for preparing an SERS substrate compounded with gold nanoparticles based on a reduction method. According to the method, an amination process is realized through modification for the surface of a silicon wafer, and then through the aurichlorohydric acid solution reduction method, the gold nanoparticles are uniformly adsorbed on the substrate to prepare the repeatable SERS substrate with high reinforcement factors. The SERS active substrate prepared by the method has the advantages of simple and feasible preparation process, high repeatability, large reinforcement factor content and the like, and has the application potential of detection of small and large molecules.