<p>Foxing is a rust-colored discoloration that is difficult to eliminate and seriously impairs the aesthetics and durability of ancient books. Due to the ultralow substance content and the constraints of conventional detection methods, the composition and causes of foxing are still unclear. Our research analyzed foxing in a book of the Republic of China era through various omics techniques and biochemical tests. The results showed that amino acids, reducing sugars, and acidic substances were enriched in foxing regions. Mixtures of reducing sugar and amino acids resulted in foxing-like spots, suggesting that the development of foxing was related to the Maillard reaction. Besides, microbial community analysis revealed that bacteria was related to foxing. Our research revealed the compound profile of foxing in ancient Chinese handmade paper for the first time. The results supported the view that foxing is related to the Maillard reaction and suggested that microbial activities may promote its formation.</p>