Three steviol glycosides (SGs) with distinct molecular structures-rebaudioside A (Reb A), stevioside (STV), and rebaudioside M (Reb M)-were selected to systematically investigate their binding behaviors with two major soy protein components, glycinin (11S) and β-conglycinin (7S), in aqueous solutions. Furthermore, the impact of these interactions on the sensory properties of SGs was explored. The results indicated that SGs formed complexes with proteins primarily through hydrogen bonding and hydrophobic interactions, with their binding affinity dually regulated by the molecular structure of SGs and the subunit structure of proteins. Specifically, Reb M, with the highest number of sugar moieties, exhibited the strongest binding capacity, followed by Reb A, with STV showing the weakest affinity. Notably, the binding ratios for all SG concentrations were below 20%. Regarding the two protein fractions, 11S showed a higher binding capacity for SGs than did 7S. Sensory evaluation revealed that SG sweetness was regulated by soy proteins in solutions in a concentration-dependent manner. Binding with 0.1% soy proteins mitigated the negative sensory attributes of Reb A and STV at a low concentration (0.1%) without significantly compromising their sweetness intensity. At a medium SG concentration (0.3%), it slightly attenuated the sweetness intensity of the three SGs but still inhibited some negative attributes of Reb A and STV. However, at a high SG concentration (0.5%), the masking effect on the bitterness and astringency was limited.