Conflicting evidence still exists regarding Vitamin B12's involvement in coronary heart disease (CHD). There is no precedent for previous studies to include both Vitamin B12, Vitamin B6, as well as Vitamin E in the consideration of CHD associating factors. Our data derived from the National Health and Nutrition Examination Survey (NHANES), which covers the period 2003-2020. 33,640 samples were included in this cross-sectional study. We used an unadjusted covariates and three adjusted covariates. The intake percentage of Vitamins E, B6, and B12 was categorized into continuous and categorical variables using multivariate logistic regression analysis and subgroup logistic regression. To estimate these trends, we applied the percentage categories of Vitamin E, B6, and B12 intake as continuous variables. We recorded Vitamin E, B6, B12, age, race, BMI, gender, household annual income, education level, hypertension status, diabetes status, smoking status, and drinking status for included samples. Multivariate regression analysis revealed that Vitamin E and B6 were negatively associated with CHD and exerted protective effects, while Vitamin B12 had little correlation with CHD. Based on the quartiles of Vitamin E and Vitamin B6 percentage, the strongest protective effect was observed in the third quartile (Q3). Analyses of subgroups showed the effects of Vitamin B6 and Vitamin E on CHD were more noticeable in women, the participant's BMI was in the 25-30 range, and participants who smoked. We identified the possible protective effect of Vitamin E and Vitamin B6 against CHD, especially in female, obese, and smoking populations, whereas income and education were also viewed as influencing factors that could be taken into account.