Background: Whether beverage consumption pattern is associated with risk of metanolic syndrome (MetS) and stroke is of public health interest. Methods: We examined the associations between the healthy beverage index (HBI) scores with prevalence of MetS and stroke among 4162 participants aged 20-80 years from the National Health and Nutrition Examination Survey (2013-2014) in U.S. Binary logistic regression was used to estimate odd ratios (OR) and 95% confidence intervals (95% CI), while adjusting for potential confounders and stratifying by gender. Results: For the prevalence of stroke, there was an inverse association between HBI scores and stroke (adj. OR for Q4 versus Q1: 0.47; 95% CI: 0.27–0.81), and gender stratified models were similar. However, there was a positive association between HBI scores and MetS (adj. OR for Q4 versus Q1: 1.38; 95% CI: 1.46–1.79) in the total participants, and gender stratified models were different. Higher HBI scores was associated with lower prevalence of MetS in females (adj. OR for Q4 versus Q1: 0.95; 95% CI: 0.65–1.38), but with higher prevalence of MetS in males (adj. OR for Q4 versus Q1: 2.02; 95% CI: 1.37–2.99). Further analyses demonstrated differences in the association of SSBs, coffee and tea, alcohol, diet drinks and full-fat milk consumption with MetS and stroke in the total subjects, males and females. Conclusions: Our findings suggested that the HBI scores was a negative association with stroke in a representative U.S. population, and the higher HBI scores was associated with increased prevalence of MetS in males but decreased in females, which may be caused by the same beverage may play a different role in the prevalence of MetS and stroke in the total participants,males and females.