To complement literature-based historical knowledge of the eating habits of 17th- and 18th-century Japan, we analysed carbon and nitrogen isotope ratios (δ13C and δ15N, respectively) of human hairs embedded in cover paper of Japanese books printed during 1690s–1890s, taking regional and temporal variations into consideration. We purchased 24 book sets from second-hand book markets. Twenty-three sets contained enough human hairs, which were non-destructively extracted from the thick, recycled paper of the book covers and used to measure the δ13C and δ15N values, found to be identical within each book set. Relatively low δ13C values and high δ15N values suggested that people depended on rice, C3 vegetables, and fish, more exclusively than contemporary Japanese people. The relatively high δ13C values found in Edo (Tokyo) might be associated with the preference for C4 millets by Edo people as a measure against beriberi (locally recognised as the Edo affliction). The δ15N values gradually increased over 200 years, indicating an increase in the contribution of marine fish both as food and fertiliser for rice fields as suggested by literature-based studies. Further collection of hairs from books will enable a thorough examination of regional and temporal variations to better understand the pre-globalised food culture.