Each spiny bur of Cenchrus spinifex Cav. (field sandbur) typically contains two seeds: a relatively large seed resembling a mango (M-type seed), and a relatively small seed resembling a pear (P-type seed). Metabolic variations arising from seed heteromorphism are regarded as crucial adaptive strategies enabling plants to thrive in unpredictable conditions. Nevertheless, metabolic studies on C. spinifex remain scarce. In this study, we utilized an untargeted metabolomics analysis by UHPLC-MS/MS to delineate the metabolic profiles associated with water deficit stress response in M- and P-type seedlings of C. spinifex. Seedlings were exposed to three watering regimes equating to 65-70 %, 45-50 %, and 25-30 % soil water-holding capacity. M-type seedlings prioritized root biomass allocation under stress, while P-type seedlings favored spikelet production, reflecting divergent survival-reproduction trade-offs. Metabolomic profiling revealed 43 differentially accumulated metabolites, with flavonoids as key discriminators between seedling types. In summary, C. spinifex exhibits pronounced metabolic divergence under water deficit stress, with flavonoids and free fatty acids serving as central adaptive metabolites. Crucially, flavonoids emerged as the key differential factor between M- and P-type seedlings. These findings demonstrate that seed heteromorphism in C. spinifex drives differential metabolic and allocation strategies, enhancing drought resilience and invasion success in arid environments.