Study on the impact of pollutants on cultural materials in storing or displaying micro-environment in museum is considered as very important for the preservation of cultural relics and its aging prevention. This paper applied the Fourier transform infrared (attenuated total reflection) technique to assess silk structural changes under volatile organic acids (formic acid/acetic acid)， which usually come from decorative materials emission and commonly exist in the surface or around cultural materials. The focus of this work was on investigating the changes of peptide bond in the area of amide Ⅰ-amide Ⅲ , as well as the peptide chains (GlyAla)n characteristic region. The structural and conformational changes in silk fiber treated with gaseous formic and acetic acid were assessed. The results indicate that both the gaseous acids can weaken the intermolecular hydrogen bond in fiber peptide, based on the spectral changes in the increased intensity of amide Ⅰ (1 617 cm-1) , the narrowing amide Ⅱ peak (1 515 cm-1), the increased intensity of random coil conformation in amide Ⅲ peak (1 230 cm-1), and the decreased fiber crystallinity as well. The obvious secondary structural conformation occurred when the concentration of gaseous formic acid reached 8.1 mg·m-3 in simulated environment. The conformational transformation was supported by the observation of the rapidly reduced random coil conformation, the increased short peptide chains (GlyAla)n with β-sheet conformation characteristic peak (1 000, 975 cm-1), and the enhanced fiber crystallinity degree as well. In contrast, gaseous acetic acid has less impact on the amide Ⅰ and amide Ⅱ bond based on the spectral changes, but it did promote random coil conformation and decreased fiber crystallinity. This work also provides a potential application of the infrared spectroscopy in non-destructive investigation of silk in-situ.