Previous studies have shown that nanoparticles can induce autophagy, and the main approach for investigating autophagy induced by nanoparticles is via traditional methods such as TEM and biochemical assay. These methods measurements suffer from the disadvantages of complicated experimental processes, cell destruction, as well as lack of characterization of individual stages of the autophagy pathway. Surface-enhanced Raman scattering (SERS) has been extensively used in biological applications. With the combination of SERS and chemometric methods, such as principal component analysis-linear discriminant analysis (PCA-LDA), identification and distribution mapping of endosomes and lysosomes in the endocytosis of Au nanoparticles has been achieved by segregating the spectra from complex SERS data sets in the previous study. In this study, silver@gold core-shell nanoparticles (Ag@Au NPs) were synthesized by reduction of gold ions on the surface of the silver nanoparticles, and the autophagy induced by Ag@Au NPs was studied with Ag@Au NPs serving both as an autophagy inducer and as a high-performance SERS substrate. Pro-survival autophagy induced by Ag@Au NPs was proved by the western blot assay, flow cytometry and fluorescent staining. Furthermore, the autophagy pathway in Ag@Au NPs-treated cells was first elucidated by SERS combined with a modified reference-based PCA-LDA methodology. This study provides a feasible way of using SERS to elucidate the autophagy pathway induced by nanoparticles.