Plant metabolites often harbor diverse bioactivities;for hu-mans,plant-derived bioactive metabolites are indispensable for health.Moreover,plants produce these metabolites to keep themselves fit.During the domestication and im-provement of crops,humans largely focused on increased yield to support population growth.For example,large seed sizes,high seed weights,and low seed shattering were se-lected in cereal crops,whereas fruit sizes and shapes were selected in vegetable crops.However,most modem crops have lost many quality-related traits,including color,flavor,taste,and nutritional quality,in addition to biotic and abiotic stress resistance.Hence,many breeders now have con-siderable interest in improving metabolic traits (e.g.,en-hanced nutrition and defense compounds) without compromising agronomic traits (e.g.,fruit sizes).In this paper,we primarily focus on the variation in nutritional metabolites during domestication and how metabolites en-hance environmental adaptability in crops.Furthermore,we forecast how understanding plant metabolism can advance breeding for high nutritional quality food production alongside food security.