Abstract: One of the biggest challenges of modern nutrition is to supply a healthy diet for human worldwide that must suit high inter-individual variability driven by complex gene-nutrient-environment interactions.Although a lot of functional foods have appeared in support of a healthy diet,a one-size-fits-all approach to nutrition is inappropriate and new personalized functional foods are necessary. And mammalian biocomplexity necessitates the incorporation of systems biology technologies into contemporary nutritional research. The paper reviews application of metabolomics in screening of new functional ingredients,assisting diet intervention studies,understanding food and metabolism interactions and nutritional epidemiology. It will provide new ideas and methods for development of personalized functional food and contribute more to prevent disease and ensure human health.