Natural materials consisting of protein structures impregnated with a tiny amount of metals often exhibit impressive mechanical behavior, which represents a new design paradigm for the development of biomimetic materials. Here, we produced Al-infiltrated silks by applying a modified Al2O3 atomic layer deposition process to the dragline silk of the Nephila pilipes spider, which showed unusual mechanical properties. The deformation behavior of the molecular structure of the Al-infiltrated silk was investigated by performing in situ Raman spectroscopy, where Raman shifts were measured concurrently with macroscopic mechanical deformations. For identifying the role of the infiltrated Al atoms, the study was performed in parallel with untreated silk, and the results were compared. Our experimental results revealed that superior mechanical properties of the Al-infiltrated silk are likely to be caused by the alterations of the sizes of the β-sheet crystals and their distribution.