Saxitoxin (STX) is a marine biotoxin produced by cyanobacteria and methanobacteria, which is harmful to humans and aquatic organisms. Therefore, it is urgent to establish an efficient, sensitive and selective method for the screening of STX. In this paper, based on the HAuCl4/H2O2 reaction system, gold nanoparticles (Au NPs) decorated Fe3O4 magnetic beads (Fe3O4@Au NPs) and Pt/Au nanozymes (Pt/Au NZs), an improved surface-enhanced Raman scattering (SERS) aptasensor was proposed for sensitive and selective detection of STX. Firstly, SERS tag (4-mercaptobenzoic acid) and aptamer modified Fe3O4@Au NPs were hybridized with complementary DNA modified Pt/Au NZs (Pt/Au-cDNA) to form the specific complexes. Wherein, aptamer acted as capture agent to specifically recognize STX, Pt/Au NZs catalyzed HAuCl4/H2O2 reaction to enhance SERS signal, and Fe3O4 facilitated the magnetic separation and simple detection operations. The SERS aptasensor achieved sensitive detection of STX with a wide linear range from 0.02 to 0.8 μmol/L and a low limit of detection (LOD) of 13 nmol/L (signal-to-noise (S/N) = 3). To evaluate the performance of this method, STX were detected in the spiked seafood samples with recoveries from 78.75% to 150% with relative standard deviation below 6.52%. Besides, the SERS aptasensor behaved good stability and repeatability, revealing its promising potential in STX detection and food safety detection.