This study prepared buckwheat protein (BP)/soybean soluble polysaccharides (SSPS) nanoparticles for PTS encapsulation, exhibiting nanocomplexes with sizes of under 300 nm, spherical particles and strong negative charge (−20 ∼ −40 mV). Moreover, the addition of SSPS enhanced the embedding effect of PTS from 61.38% to 89.78%. X-ray and fluorescence spectroscopy revealed that PTS can bind to BP and SSPS. Molecular docking analysis showed PTS can bind to BP with hydrogen bonds and hydrophobic bonds at pH 7.0, only can bind with hydrophobic bonds at pH 4.5. Stability experiments revealed that nanocomplex had higher physical and foam stability. Antioxidant experiments revealed that antioxidant capacity of PTS in the nanocomplex was significantly higher than that in the free state. Therefore, the research findings can be advantageous to the utilization of PTS in functional foods.