The structure of polyphenolic compounds plays a pivotal role in determining their functional efficacy. Moreover, the presence of bile salt surfactants can significantly impact their metabolism. Hence, this study employed multi-spectroscopic methods to explore the binding mechanism of Quercetin (Que) and Taxifolin (Tax, dihydroquercetin) with bovine hemoglobin (HB), influenced by the addition of sodium taurodeoxycholate (NaTDC). The results indicate that, through the static quenching mechanism, nearly a single Que. or Tax molecule can spontaneously form a complex on each HB chain. This process is driven by Van der Waals forces, hydrophobic interaction, and hydrogen bonds. During the interaction, the secondary structure of HB chains undergoes changes with an enhanced hydrophobicity. The hydrogenation of C2C3 double bond of flavonols increases the structural flexibility and helps to close to the active sites of HB, resulting in the stronger binding affinity of Tax on HB chains than Que. Additionally, the presence of this double bond exerts a notable influence on the physicochemical properties of polyphenols, such as solubility, antioxidant activity, and antibacterial activity. Specifically, the solubility of pure Tax in water, and its bacteriostatic effect against Klebsiella Pneumoniae (KP) and Methicillin-resistant Staphylococcus Aureus (MRSA), are superior to that of Que. The C2C3 double bond of Que. make it exhibiting better antioxidant ability than Tax. After interacting with HB, the antioxidant capacity are enhanced, and the bacteriostatic effects are either weakened or remain essentially unchanged compared to those of pure Que./Tax. The addition of NaTDC can enhance the low solubility of Que./Tax and regulate their interaction strength with HB, thereby further influencing their bioavailability. For the Tax/Que-HB mixed system, the presence of NaTDC strengthens their antioxidant capacity, but does not affect the antimicrobial activity basically. These findings hold significant practical implications for enhancing the therapeutic efficacy and bioavailability of natural products.