This study conducted data on 15,446 adults to explore the impact of flavonoids on weight-adjusted waist index (WWI). This was a nationwide cross-sectional study among US adults aged 20 years or older. Dietary intake of flavonoids was assessed through 24-h recall questionnaire. WWI was calculated by dividing waist circumference (WC) by the square root of weight. We utilized weighted generalized linear regression to evaluate the association between flavonoids intake and WWI, and restricted cubic splines (RCS) to explore potential non-linear relationships. Our findings indicated that individuals with lower WWI experienced a notable increase in their consumption of total flavonoids, flavanones, flavones, flavan-3-ols, and anthocyanidins intake (β (95% CI); −0.05(−0.09, −0.01); −0.07(−0.13, 0.00); −0.07(−0.11, −0.02); −0.06(−0.11, 0.00); −0.13(−0.18, −0.08), respectively), with the exception of flavonols and isoflavones. Additionally, consumption of total flavonoids, flavonols, flavanones, isoflavones, and flavan-3-ols had a non-linear relationship with WWI (all P for non-linearity < 0.05). Furthermore, the effect of total flavonoids on WWI varied in race (P for interaction = 0.011), gender (P for interaction = 0.038), and poverty status (P for interaction = 0.002). These findings suggested that increase the intake of flavonoids might prevent abdominal obesity, but further prospective studies are requested before dietary recommendation.