Obesity is a chronic disease that profoundly impacts human health, and the role of plant-based formulas (PBFs) in combating obesity has garnered significant interest. Studies have revealed that fermentation significantly enhances the taste, aroma, quality, and health benefits of PBF water extract, with pasteurization being the preferred sterilization technology. However, few studies have investigated the effects of pasteurization on the active components and potential functions of PBF water extract fermentation broth. To examine the impact of pasteurization on fermented water extract of Millettia speciosa Champ (FH08F) and its potential anti-obesity properties, the components of FH08F and thermal-pasteurized FH08F (FH08FS) were analyzed in this study. The analysis revealed a substantial rise in ester content following sterilization. This can be attributed to the acidic environment that promotes the esterification reaction during the heating phase. Network pharmacology was employed to thoroughly examine seven active components of upregulated compounds (URCs) with potential obesity targets, which constituted 92.97% of the total URC content, and four of them were nitrogen-containing aromatic heterocyclic compounds (NAHCs), which accounted for 90.33% of the total URC content. Upregulated NAHCs appear to actively contribute to efficacy against obesity. Molecular docking analyses have shown that theophylline, an NAHC, has the strongest binding affinity with the obesity-related target PTGS2 (Prostaglandin G/H synthase 2, 5FLG). These results imply that theophylline may directly activate PKA/PKG-mediated phosphorylated hormone-sensitive lipase (p-HSL), thereby promoting lipolysis through the cAMP signaling pathway and stimulating the catabolism of triglycerides (TGs) to combat obesity. In conclusion, pasteurization substantially alters the composition of FH08F, and NAHCs are likely to play a significant role in its potential anti-obesity function. These findings provide a scientific foundation for the potential therapeutic effect of FH08FS on obesity and associated metabolic diseases.