Steviol glycosides (SG) are characterized by high sweetness intensity and low energy contribution. However, their bitter taste and persistent aftertaste have limited their application. To alleviate the bitterness and persistent aftertaste of SG, nanoscale complex coacervates were constructed using phytic acid (PA) and chitooligosaccharides (COS), and their effects on SG bitterness perception and the apparent dialyzable behavior of its major components were investigated. PA-COS complex coacervates were prepared by regulating the molar ratio of PA to COS and the pH of the system. Their physicochemical properties and intermolecular interactions were characterized, and their effects on SG bitterness and the apparent dialyzable behavior of stevioside (STV), rebaudioside A (RA), and rebaudioside C (RC) were evaluated using sensory evaluation and dialysis-high performance liquid chromatography. The results showed that nanoscale PA-COS complex coacervates were formed at relatively high PA ratios under acidic conditions, with an average particle size of 188.00 nm. Noncovalent interactions, including electrostatic interactions and hydrogen bonding, were identified between PA and COS. When the PA:COS molar ratio was 5:1, the peak bitterness intensity of SG was reduced by 40.00%, and the bitterness duration was shortened by 6.00 s. The apparent dialyzable behavior of STV, RA, and RC was altered by PA-COS, with the peak area of STV being reduced by 38.69%. In conclusion, the bitterness of SG was reduced and the apparent dialyzable behavior of its major components was altered by nanoscale PA-COS complex coacervates, providing a potential theoretical basis for the modulation of the flavor of natural high-intensity sweeteners through molecular assembly of natural food components.