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The potential application of Xylocarpus granatum, a mangrove species, as traditional medicine has been widely linked to its high secondary metabolite and antioxidant contents. However, few studies have been reported to identify and classify active metabolites responsible for such excellent biological activities. Therefore, the aim of this work was to determine the antioxidant activity, identify the metabolite profiles, and predict the metabolites acting as antioxidants in X. granatum extract using a gas chromatography–mass spectrometry (GC-MS)-based metabolomics approach. The seeds, stems, fruit peel, pulp, leaves, and twigs of X. granatum were macerated with ethanol. Each extract was analyzed with GC-MS, and the data were processed using mass spectrometry data-independent analysis (MS-DIAL) software to identify the metabolites. The IC50 value of plant parts of X. granatum ranged from 7.73 to 295 ppm. A total of 153 metabolites were identified and confirmed in the X. granatum extracts. Among the identified metabolites, epicatechin and epigallocatechin were the two most abundant in the stem extracts and are expected to have the greatest potential as antioxidants. Principal component analysis (PCA) succeeded in grouping all parts of the plant into three groups based on the composition of the metabolites: group 1 (stems, fruit peel, and twigs), group 2 (seeds and pulp), and group 3 (leaves).