Surface-enhanced Raman scattering (SERS) technique is a powerful assay due to its high sensitivity, rapid detection, and fingerprint vibration specificity. Magnetic nanoparticle composite-based SERS strategy presents additional merits of easy magnetic enrichment of sample, detection selectivity improved via magnetic separation and excellent sensitivity reached by magnetic inducing optimization of localized surface plasmon resonance fields to generate more hot spots. In this review, we introduce the preparation and classification of magnetic SERS substrates, surface functionalization strategies, the mechanism of magnetic inducing optimization SERS and then focus on their recent applications in the fields of food safety inspection, biomedical detection, and environmental analysis. As a perspective, metal salt-based spinel ferrites as promising strong magnetic substrates need to be concerned to advance magnetic optimization effect in SERS detection because of easy magnetic preparation, tolerance in chemical media, and the long-term stability during storage. Challenges and opportunities in magnetic substrate-based SERS assays are also discussed.