A high-throughput, rapid, and highly sensitive surface-enhanced Raman spectroscopy (SERS) microarray for screening multiple mycotoxins has been developed on a three-dimensional silver nanoparticle porous silicon (3D AgNP-Psi) SERS substrate, which was easy to be engineered by electrochemical etching and magnetron sputtering technology. The etching current density, etching waveform, and target material for magnetron sputtering have been investigated to obtain an optimal 3D SERS substrate. The optimized 3D AgNP-Psi SERS substrate showed an enhancement factor of 2.3 × 107 at 400 mA/cm2 constant current density etching for 20 s and Ag target magnetron sputtering for 200 nm thickness on the surface of Psi. The simulation electric field distribution showed the near-field enhancement can reach 3× higher than that of AuNPs. A protein microarray has been designed to screen multiple mycotoxins by AuNP Raman tags and a competitive immunoassay protocol on the surface of the 3D SERS substrate. The SERS protein microarray displayed wide linear detection ranges of 0.001-100 ng/mL for ochratoxin A, 0.01-100 ng/mL for aflatoxin B1, 0.001-10 ng/mL for deoxynivalenol, along with pg/mL low limit of detection, good recovery rates, repeatability, and reproducibility. The 3D SERS protein microarray is easily engineered and has a great potential application in medicine, environment, and food industry fields.