Pomegranate peel polyphenols (PPPs) are recognized as promising food additives due to their diverse bioactivities; however, their application is limited by poor stability. To address this critical issue, three types of PPPs microcapsules were prepared using β-cyclodextrin (CD), whey protein isolate (WPI), and a composite material of CD-WPI through ultrasound treatment (US). Results revealed that ultrasound treatment can enhance the PPPs-wall material interaction, as evidenced by MD simulations. The encapsulation efficiency of CD-WPI-PPPs was 93.73 %, which was significantly higher than that of CD-PPPs and WPI-PPPs (p < 0.05). The degradation rate constant of CD-WPI-PPPs was reduced by 95.83 %, and its t1/2 was extended by 23-fold compared to that of unencapsulated PPPs. Furthermore, CD-WPI-PPPs exhibited greater DPPH scavenging activity and inhibited polyphenol release during oral and gastric digestion while promoting release during intestinal digestion. These outcomes were attributed to enhanced integrity and interactions between PPPs and composite materials in the microcapsules formed through ultrasound treatment, as supported by SEM images and FT-IR spectra. Consequently, the application of US in the preparation of PPPs microcapsules presents a promising strategy for developing natural nutrient additives for food applications, thereby enhancing the functional properties of food products.