Background: We aim to examine the relationship between age at menarche and hyperhomocysteinemia in women in Hunan Province. Methods: Participants were required to complete a questionnaire that included age at menarche, lifestyle habits, other baseline information, and blood biochemical parameters in a cross-sectional study. The association between hyperhomocysteinemia and age at menarche was examined by Multivariable adjusted logistic regression. Results: A cohort of 2008 women with a mean age of 60.11 years (aged from 18.0 to 88.0 years) was included in this study. After adjustment for confounding factors such as age, the results showed that the risk of hyperhomocysteinemia among women whose age at menarche were over 16 years was 2.543 (1.849, 3.469) times higher than the risk among women whose age at atmenarche were less than 14 years, and 2.656 (1.882, 3.748) times more likely to have hypertension than women with menarche at 14 years. Besides, the odds ratios of diabetes, hyperlipidemia, and obesity were elevated in women older than 16 years of age at menarche (OR = 1.924, p 0.001; OR = 1.491, p = 0.014; OR = 1.670, p = 0.022). Conclusions: Our findings suggest that late menarche tends to be associated with a high risk of hyperhomocysteinemia and its associated set of diseases such as hypertension, diabetes, hyperlipidemia, and obesity in women in Hunan, China. This association tends to differ across birth cohorts. Therefore, adequate attention of menarcheal age may be able to predict diseases in elderly females.