The reversed-phase high-performance liquid chromatographic (RP-HPLC) behavior of some newly synthesized hydroxythioxanthone derivatives using binary acetonitrile–water mixtures as mobile phase has been examined. First, the variation in the retention time of each molecule as a function of mobile phase properties was studied by Kamlet–Taft solvatochromic equations. Then, the influences of molecular structure of the hydroxythioxanthone derivatives on their retention time in various mobile phase mixtures were investigated by quantitative structure–property relationship (QSPR) analysis. Finally, a unified model containing both the molecular structure parameters and mobile phase properties was developed to describe the chromatographic behavior of the systems studied. Among the solvent properties, polarity/polarizability parameter ( π *) and hydrogen-bond basicity ( β), and among the solute properties, the most positive local charge (MPC), the sum of positive charges on hydrogen atoms contributing in hydrogen bonding (SPCH) and lipophilicity index (log P) were identified as controlling factors in the RP-HPLC behavior of hydroxythioxanthone derivatives in actonitrile–water binary solvents.