Baishouwu, derived from Cynanchum auriculatum (CA) Royle ex Wight, Cynanchum bungei (CB) Decne., and Cynanchum wilfordii (CW) (Maxim.) Hemsl., is a valuable traditional Chinese medicine. CA is also recognized as a new food resource by China's National Health Commission. Given the considerable variations in flavor and chemical composition among these species and lack of their qualitative assessments, accurately differentiating between the species constituting Baishouwu is essential. To develop a method combining electronic tongue (E-tongue), electronic nose (E-nose), and ultra-performance liquid chromatography-quadrupole-time of flight/mass spectrometry (UPLC-Q-TOF/MS) to differentiate between Baishouwu samples. Fifteen batches of Baishouwu samples were analyzed using E-tongue, E-nose, and UPLC-Q-TOF/MS. Flavor differences and key differential metabolites were determined through principal component analysis and orthogonal partial least squares discriminant analysis. E-tongue results revealed umami, sweetness, and richness as the predominant flavors of Baishouwu, with CA having the highest umami response, CW exhibiting the highest bitterness, and CB the highest sweetness. E-nose sensors showed consistent responses across species, with variations in signal strength; W1W and W2W sensors showed the highest response values. A total of 158 and 41 characteristic variables in the positive and negative ion modes, respectively, were selected as candidate differential metabolites, of which 29 and 14 were confirmed through database comparison. Eight critical differential metabolites, including C21 steroids and acetophenone compounds, were identified. This study presents a strategy for differentiating among the species constituting Baishouwu, providing a basis for broader application and establishing quality standards for these medicinal compounds.