The low bioavailability of polyphenolic compounds due to poor solubility and stability is a major challenge. Encapsulation of polyphenols in zein-based composite nanoparticles can improve the water dispersion, stability, targeted delivery, and controlled release of polyphenols in the gastrointestinal tract. In this study, we investigated the fluorescence properties, bioactivity, and microstructural characteristics of polyphenols during digestion, revealing that zein nanoparticles protect polyphenols from gastric degradation and promote their sustained release in the small intestine. The effects of different ionic species and salt ion concentrations on the digestive properties of polyphenol complex delivery systems have also been explored. In addition, the formation of “protein corona” structures during digestion may affect bioavailability. These findings highlight the potential of nanoparticle formulations to improve polyphenol stability and absorption. The results of this study may provide new insights and references for the study of polyphenol bioavailability enhancement.