As manganese ions (Mn2+) are identified as an environmental risk factor for neurodegenerative diseases, uncovering their action mechanism on protein amyloid fibril formation is crucial for related disease treatments. Herein, we performed a combined study of Raman spectroscopy, atomic force microscopy (AFM), thioflavin T (ThT) fluorescence, and UV-vis absorption spectroscopy assays, in which the distinctive effect of Mn2+ on the amyloid fibrillation kinetics of hen egg white-lysozyme (HEWL) was clarified at the molecular level. With thermal and acid treatments, the unfolding of protein tertiary structures is efficiently accelerated by Mn2+ to form oligomers, as indicated by two Raman markers for the Trp residues on protein side chains: the FWHM at 759 cm-1 and the I1340/I1360 ratio. Meanwhile, the inconsistent evolutionary kinetics of the two indicators, as well as AFM images and UV-vis absorption spectroscopy assays, validate the tendency of Mn2+ toward the formation of amorphous aggregates instead of amyloid fibrils. Moreover, Mn2+ plays an accelerator role in the secondary structure transition from α-helix to organized β-sheet structures, as indicated by the N-Cα-C intensity at 933 cm-1 and the amide I position of Raman spectroscopy and ThT fluorescence assays. Notably, the more significant promotion effect of Mn2+ on the formation of amorphous aggregates provides credible clues to understand the fact that excess exposure to manganese is associated with neurological diseases.