Proteins perform vital functional and structural duties in living systems, and the in-depth investigation of protein in its native state is one of the most important challenges in the postgenomic era. Surface-enhanced Raman spectroscopy (SERS) can provide the intrinsic fingerprint information of samples with ultrahigh sensitivity but suffers from the reproducibility and reliability issues. In this paper, we proposed an iodide-modified Ag nanoparticles method (Ag IMNPs) for label-free detection of proteins. The silver nanoparticles provide the huge enhancement to boost the Raman signal of proteins, and the coated iodide layer offers a barrier to prevent the direct interaction between the proteins and the metal surface, helping to keep the native structures of proteins. With this method, highly reproducible and high-quality SERS signals of five typical proteins (lysozyme, avidin, bovine serum albumin, cytochrome c, and hemoglobin) have been obtained, and the SERS features of the proteins without chromophore were almost identical to the respective normal Raman spectra. This unique feature allows the qualitative identification of them by simply taking the intensity ratio of the Raman peaks of tryptophan to phenylalanine residues. We further demonstrated that the method can also be used for label-free multiplex analysis of protein mixture as well as to study the dynamic process of protein damage stimulated by hydrogen peroxide. This method proves to be very promising for further applications in proteomics and biomedical research.