SummaryIn today's consumer landscape, the health benefits of preserved foods, particularly pickled and salted mustard greens, are gaining recognition on a global scale. To compare health‐promoting compounds between fresh and preserved mustard greens, a comprehensive assessment using proximate composition analysis and untargeted metabolomics was conducted. The sub‐metabolome data revealed distinct profiles for each type of mustard greens, clearly seen in their separation through principal component analysis. The metabolite profiling identified 37 metabolites with significant differences (P‐value < 0.05, −log10 P‐value > 4). Fresh mustard greens were found to be rich in 16 identified metabolites, including sulfonic acids, purines, oxepanes, monosaccharides, fatty acids, amino acids and tripeptides, offering antioxidants, gut enhancers and immune boosters. In contrast, pickled mustard greens exhibited an abundance of 20 identified metabolites in the classes of flavonoids, amino acids and dipeptides, providing antioxidant properties. Salted mustard greens, on the other hand, primarily showcased a high level of uridine diphosphate glucose (a pyrimidine class metabolite), supporting glycoconjugate synthesis among all samples. This study highlights the prominent presence of various classes of metabolites associated with health‐benefit compounds in fresh and preserved mustard greens. These insights contribute to the evaluation of health benefits in the food industry when choosing between pickled and salted preservation methods.