Abstract: Sanhuang decoction, a traditional Chinese medicine prescription, was firstly described in Golden Chamber by Zhang Zhongjing in the Han Dynasty, and has been used clinically for thousands of years to treat diabetes and obesity. However, the specific bioactive compounds being responsible for the hypoglycemic and hypolipidemic effects of Sanhuang decoction and the underlying therapeutic mechanism remain elusive, and further research efforts are in great need. Hence, the aim of this study was to discover the potential hypoglycemic and hypolipidemic phytochemicals in Sanhuang decoction and to explore their potential mechanisms of action. Here, the in vitro α-glucosidase (α-Glu) and lipase (LP) inhibitory activities of Sanshuang decoction were determined, and the results showed that Sanhuang decoction possesses significant α-Glu and LP inhibitory activities in vitro. Then, 24, 17 and 25 potential bioactive ligands in Sanhuang decoction are successfully captured by combining affinity ultrafiltration liquid chromatography-mass spectrometry with three drug targets, namely α-Glu, α-amylase (α-Amy) and LP, respectively. These potential bioactive ingredients fished out from Sanhuang decoction exhibit various binding capacities to α-Glu, α-Amy and LP, respectively. Thereof, epicatechin-3-O-gallate possesses significant hypoglycemic and hypolipidemic effects. Finally, some representative active ligands were further verified with molecular docking assay, and the molecular docking results are consistent with those of affinity ultrafiltration. Furthermore, in addition to hydrogen bond (H-bond), there are various other interaction forces between these potential bioactive ingredients and their corresponding target enzymes, such as Pi-Sigma, Pi-Pi T-shaped and Pi-Alkyl interactions. In this study, the potential hypoglycemic and hypolipidemic constituents in Sanshuang decoction were explored and identified by using affinity ultrafiltration liquid chromatography-mass spectrometry with three drug targets tightly correlating to the metabolisms of blood sugar and lipids in the human body, and the effective material basis of Sanshuang decoction can thus be preliminarily clarified. In this way, the interaction network among these bioactive compounds and three drug targets were constructed, thus providing theoretical support for the clinical applications of Sanhuang decoction for the treatments of obesity and diabetes.