Accumulation of Zn2+ ions in protein aggregates has been suggested to be a key factor in Alzheimer’s disease etiology. However, the specific influence of Zn2+ ions on the formation of amyloid fibrils or amorphous aggregates is still much debated. Herein, we conducted a combined study of Raman spectroscopy, UV–vis absorption spectroscopy and ThT fluorescence assay on the concentration effects of Zn2+ ions on amyloid fibrillation of hen egg-white lysozyme with thermal treatment. The addition of Zn2+ ions showed a negligible effect on unfolding of the protein tertiary structures and nucleation pathways on amyloid fibrillation. In contrast, a distinct concentration-dependence was observed for the influence of Zn2+ ions on the transformation of lysozyme secondary structures. At low concentration, the metal ions do not affect the populations of major secondary structures in the final state after incubation, while they at high concentration exhibit a promotion effect on the transformation from α-helix to β-sheet-like structures. These findings provide insights into the multifaceted impact of Zn2+ ions on protein aggregation, shedding light on potential therapeutic strategies for neurodegenerative diseases.