Controlling starch digestibility through natural dietary components has become an effective approach to mitigate postprandial hyperglycemia. Polyphenols are known to interact with starch and digestive enzymes via non-covalent forces, yet the role of phenolic hydroxyl number and electrostatic potential in these interactions remains poorly understood. In this study, Cyperus esculentus (tigernut) starch was selected as a starch source to prepare RS5-type complexes with four flavonols—galangin (three hydroxyls), kaempferol (four hydroxyls), quercetin (five hydroxyls), and myricetin (six hydroxyls)—to elucidate the effect of hydroxyl number on complex structure and α-amylase inhibition. The complexes were characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), and differential scanning calorimetry (DSC). Results showed that increasing the number of phenolic hydroxyl groups enhanced electrostatic potential distribution and hydrogen bonding, leading to reduced crystallinity, improved thermal stability, and increased RS5 content. Kinetic analysis and molecular simulations revealed that polyphenols with higher hydroxyl numbers exhibited stronger electrostatic interactions with key catalytic residues (Asp197, Asp300, Glu233) and aromatic residues (Trp58, Trp59, Tyr62) in α-amylase, resulting in greater inhibition and enzyme conformational distortion. Density functional theory (DFT) mapping confirmed that enhanced negative electrostatic potential regions facilitated tighter binding. These findings provide new insight into how phenolic hydroxyl number and electrostatic potential cooperatively regulate starch structure and enzyme inhibition, offering a theoretical foundation for developing polyphenol-based low-glycemic foods.