The importance of obesity as a factor that increases the probability of migraine episodes is increasingly acknowledged. Thus, this study aimed to explore the potential correlation between central obesity and migraine, emphasizing the waist-to-height ratio (WHtR) as a key measure in assessing this relationship. This cross-sectional analysis included 13,344 individuals who participated in the National Health and Nutrition Examination Survey (NHANES) from 1999-2004. To investigate the association associations between WHtR and migraine, we utilized refined multivariate logistic regression models, smoothing curve fitting methods, subpopulation analysis, and interactive testing. Of the 13,344 participants, 2,764 (20.72%) had migraines. A significant positive correlation was observed between the WHtR and migraine incidence in both the partially adjusted model (3.08 [95% CI: 1.92-4.94]) and the crude model (1.95 [95% CI: 1.23-3.08]). The participants in the highest quartile of the WHtR had a 13% greater incidence of migraine than those in the lowest quartile [1.13(0.99,1.28)]. The interaction analysis revealed a statistically significant difference (p<0.01) in this relationship among the subgroups. Notably, the correlation between WHtR and migraine risk was not significant and negative in patients ≥60 years, indicating that obesity has a mitigating role in preventing migraine in this elderly population. The incidence of migraine increased concomitantly with increased WHtR. However, central obesity has a protective effect against migraine occurrence in individuals ≥60 years. Thus, our findings underscore the importance of WHtR in migraine prevention and management strategies and highlight its potential as a critical biomarker for mitigating migraine incidence.