Hydroxycarboxylic acids, viz., α-hydroxyisobutyric acid (HIBA) and mandelic acid (MA), have been widely employed as eluents for inner transition metal separation studies. Both extractants have identical functional groups (OH and COOH) with different side-chains. Despite their similarities in binding motifs, they show different retention behaviors for thorium and uranium in liquid chromatography. To understand the mechanism behind the trend, a detailed study on the aqueous phase interaction of thorium with both extractants is carried out by speciation, spectroscopy, and density functional theory-based calculations. Potentiometric titration experiments are carried out to reveal the stability and species formed. Electrospray ionization mass spectrometry is performed to identify the formation of different species by Th with both HIBA and MA. It is seen that for Th-HIBA and Th-MA, the dominating species are ML3 and ML4, respectively. A similar pattern observed in potentiometric speciation analysis supports the tendency of Th to form higher stoichiometric species with MA than with HIBA. The difference in the dominating species thus helps in explaining the reversal in the retention behavior of uranium and thorium in the reverse-phase liquid chromatographic separation. The results obtained are corroborated with extended X-ray absorption fine structure spectroscopic measurements and density functional theory (DFT) calculations.