Pachyrhizus erosus (L.) Urb. is a tropical perennial vine plant native to southern Mexico, Southeast Asia, Central America, and Africa. In this study, we analyzed and identified various polyphenolic compounds and isoflavones present in ethanolic P. erosus root extracts and investigated their potential anti-obesity activity as a natural health food resource. The extraction process involved drying the yam bean, followed by extraction with 70% ethanol, evaporation, and freeze-drying. Fractionation was achieved through layer separation using n-hexane, ethyl acetate (EtOAc), butanol (BuOH), and water. The EtOAc fraction exhibited the highest antioxidant activity among the experimental groups, with an IC50 value of 531.77 µg/mL for ABTS radical scavenging. In α-glucosidase and lipase inhibition assays, IC50 values were determined to be 873.07 µg/mL and 915.02 µg/mL, respectively. Using HPLC and LC-MS/MS, we detected isoflavone components in P. erosus root extracts, identifying daidzein, genistein, and rotenone among them. Daidzein was the most abundant isoflavone in P. erosus root extracts. To validate the anti-obesity activity in the EtOAc fraction and daidzein, we used 3T3-L1 preadipocytes treated with MDI (3-isobutyl-1-methylxanthine, dexamethasone, insulin) for 8 days. Oil Red O staining experiments demonstrated a concentration-dependent reduction in lipid content in the EtOAc fraction and daidzein treatment groups. Additionally, we examined the expression pattern of proteins related to the leptin-PPAR-FAS Pathway, revealing a concentration-dependent decrease in obesity-related proteins.