Summary Polygonum minus (PM) has a rich traditional usage for health benefits, yet its potential as a natural‐based solution for obesity management remains unexplored. This study evaluated the antioxidant properties, inhibition of pancreatic lipase and α‐glucosidase activities, and metabolite profiles of PM aerial extracts harvested at 8, 10, and 12 weeks using 1H NMR‐based metabolomics. PM harvested at 12 weeks exhibited significant antioxidant and enzyme inhibition activities. NMR metabolomics unveiled nine major metabolites correlated to the bioactivities of 12‐week PM. LC–MS/MS profiling enabled the identification of flavonoids and phenolic acids, with the majority having sulfate, gallate, and glycoside moieties. Notably, in vivo experiments demonstrated that rats treated with 200 mg kg−1 and 400 mg kg−1 PM exhibited significantly lower (P < 0.05) total body weight gain (39.03% and 52.59%, respectively) compared to negative control rats (69.95%), with the lower dose group also exhibiting reduced (P < 0.05) fasting blood glucose levels. This study highlights the potential of 12‐week PM as a natural‐based solution in obesity management. [ABSTRACT FROM AUTHOR]