Cardiometabolic disease (CMD) is a major public health problem. It is well known that CMD is caused by interactions between environmental and genetic factors. Additionally, recent studies on mechanism of CMDs have demonstrated that changes in molecular intermediates (e.g. levels of metabolites and DNA methylation) affect prevalence of CMDs. However, there has been limited evidence to suggest causal effect of dietary factors on CMDs, mediated by molecular intermediates. The aim of current study is to estimate relationship between dietary factors and cardiometabolic health, considering effect of molecular mediation including levels of metabolite and DNA methylation. This study can contribute to enhance an understanding of causal effect of dietary factors on CMDs and clarify the mechanism of diet-metabolome-genome-epigenome-health outcomes and contribute to prevent CMDs.