Amino acids， vitamin E and lipids are three classes of metabolites with antioxidant activity. GC-MS， UPLC， and LC-MS/MS were used to detect the relative content of three types of metabolites in the fruits of six Citrus varieties during the ripening process to analyze the dynamic changes of amino acids， vitamin E， and lipids during the ripening process of citrus fruits and evaluate the antioxidant activity of citrus. The results showed that citrus fruits mainly accumulated serine， proline， and aspartic acid， while threonine was particularly abundant during the green fruit stage of citrus. The total content of nine amino acids in green pulp of C. chuana ‘Bendizao’ （BDZ） during the green fruit stage was the highest. For vitamin E， α- tocopherol is the main isomeric form in citrus， which accumulates abundantly in mature colored pericarp. Additionally， citrus fruits did not accumulate δ- tocopherol， and γ- tocopherol only accumulated in the colored pericarp of citrus. A total of 8 major categories （176 species） of lipids were identified and showed significant characteristics of spatiotemporal distribution in citrus fruits， with phosphatidylcholine being the main form of lipids in citrus. It was found that some amino acids are highly positively correlated with lipids through correlation analysis of the content of three types of metabolites in citrus fruits. It will have a guiding significance for the improvement of quality in citrus varieties.