This study aimed to address the issue of the low solubility in the model drug probenecid (PRO) and its impact on bioavailability. Two salts of probenecid (PRO), 4-aminopyridine (4AMP), and 4-dimethylaminopyridine (4DAP) were synthesized and characterized by PXRD, DSC, TGA, FTIR, and SEM. The crystal structures of the two salts were determined by SCXRD, demonstrating that the two salts exhibited different hydrogen bond networks, stacking modes, and molecular conformations of PRO. The solubility of PRO and its salts in a phosphate-buffered solution (pH = 6.8) at 37 °C was determined, the results showed that the solubility of PRO salts increased to 142.83 and 7.75 times of the raw drug, respectively. Accelerated stability experiments (40 °C, 75% RH) showed that the salts had good phase stability over 8 weeks. Subsequently, Hirshfeld surface (HS), atom in molecules (AIM), and independent gradient model (IGM) were employed for the assessment of intermolecular interactions. The analyses of salt-forming sites and principles were conducted using molecular electrostatic potential surfaces (MEPs) and pKa rules. The lattice energy (EL) and hydration-free energy (EHF) of PRO and its salts were calculated, and the relationships between these parameters and melting points and the solubility changes were analyzed.