Obesity is a metabolic disorder caused by an imbalance between energy intake and expenditure, often leading to excess fat and related diseases. Browning of white adipose tissue, which increases energy expenditure, is a promising anti-obesity strategy. Herbal medicines are considered safer than conventional drugs, though their fat-browning mechanisms are not fully understood. This study examined the effects of Coix lacryma-jobi and Raphanus sativus, and their active compounds, coixol and sinigrin, from Taeyeumjowui-tang. In 3T3-L1 adipocytes, Oil-Red-O staining showed that treatment reduced lipid accumulation and droplet size. The qPCR, Western blotting, and immunostaining confirmed that coixol and sinigrin upregulated browning markers (UCP1, PGC-1α, PRDM16) and beige fat genes (Cd137, Cidea, Cited1, Fgf21, Tbx1, Tmem26). They downregulated lipogenic genes (Fasn, Lpl, Srebf1, Acaca), while increasing lipolytic genes (Atgl, Hsl, Plin1) and fatty acid oxidation genes (Aco1, Cpt1, Ppara). Mitochondrial biogenesis genes (Cox4, Nrf1, Tfam) were also upregulated. Inflammation was reduced, as shown by decreased IL1b, Tnfa, and increased IL4, IL10, and IL6. Mechanistic studies revealed that fat browning was associated with β3-adrenergic receptor activation, SIRTs, and AMPK phosphorylation. These effects were enhanced by β3-AR and AMPK agonists, and blocked by their inhibitors. Overall, coixol and sinigrin promote fat browning and metabolic improvement, suggesting their potential as natural anti-obesity agents.