Natural aging plays a key role in the degradation of proteinaceous binders which are important dispersers and stabilizers of painting layers. Knowledge about the natural aging influence on the stability of binders is important for exploring the deterioration mechanisms of painted artworks. Pig glue, whole egg, egg white, egg yolk, casein, and mixtures with ultramarine were aged for 10 years in natural conditions. GC-MS and FTIR were applied to explore the changes in the binders at a molecular level. Our experiment revealed that the less stable Met (Methionine), Lys (Lysine), Ile (Isoleucine), Ser (Serine), Asp (Aspartic acid), Glu (Glutamic acid), Hyp (Hydroxyproline), especially aromatic Phe (Phenylalanine), and Tyr (Tyrosine) were damaged, thus the contents of the stable Ala (Alanine), Gly (Glycine), Val (Valine), Leu (Leucine), and Pro (Proline) increased. The broadening of Amide A and the declining amount of α-helix, along with the increasing contents of β-sheet and random coils, all showed that the binders had transformed into disordered states. What is more, we found that pig glue had better natural aging resistance, ultramarine could speed up the aging process and lipids in egg were more easily degraded. The mechanisms of the changes of primary structures and secondary structures are also discussed in the paper.