With the advancement of the conservation of ancient books and other paper cultural relics, research on the conservation of paper itself has made progress. However, by contrast, there is an urgent need to carry out studies on the preservation and conservation of writing materials such as ink and pigments on paper and their interactions. Investigation of the aging of ancient ink marks is focused on the essence of ink-paper interaction, which is of great significance for ancient book conservation. Using the ink marks on an ancient Chinese book collected in Fudan University Library as examples, we analyzed the phenomenon of ink yellowing in a multi-scale way using various non- and micro-destructive methods such as microscopic observation, surface pH testing, and micro-Raman and FT-IR spectrometry. The results show that compared with the blank fibers, the yellowed fibers at and around the ink marks lacked luster and were slightly decayed, more acidic and had more surface oxidation groups, indicating that the ink might have an impact on the aging and degradation of paper. This was further verified by a simulated aging experiment of soaking paper in ink. The results show that compared with neutral inks, acidic inks promote the aging of paper, with an obvious decline of pH value, tensile and folding properties, and a lower retention rate of degree of polymerization. The simulated aging experiment of ink characters supported the foregoing conclusions. Characters using more acidic ink had a stronger acidity and the chromatic aberration was also more significant. The above results indicate that the acidity of ink had a very important impact on the degradation of paper. In-depth research on this subject could not only reveal the mechanism of paper aging affected by ink during the preservation of ancient books, which would be helpful in understanding and formulating long-term strategies for the conservation of ancient books, but would also provide guidance for the development of ink for restoration.