Ion pairs represent a robust molecular force arising from the union of oppositely charged ions, held together by Coulomb attraction. Daidzein (Dai), categorized as a BCS IV drug, faces limitations in clinical application due to its relatively low solubility. To enhance the drug's solubility, a Dai ion pair was prepared, and the mechanism underlying ion-pair formation was investigated. A comprehensive approach, combining experimental techniques and theoretical calculations, such as scanning electron microscopy, powder X-ray diffraction, differential scanning calorimetry, Fourier-transform infrared spectroscopy, proton nuclear magnetic resonance spectroscopy, X-ray Photoelectron Spectroscopy, and computational simulation was employed to explore the ion-pair formation mechanism. The findings indicate a significant improvement in Dai solubility through the preparation of Arg and Lys ion-pair compounds. The results revealed that the Dai-Lys ion pair exhibited more short hydrogen bonds and fewer long hydrogen bonds than did the Dai-Arg ion pair, strengthening the intermolecular interactions and improving crystal structure stability. This study effectively enhanced the solubility of Dai and offers valuable insights into the mechanisms underlying ion pair formation in ionizable drugs.