Purple potato anthocyanins (PPAs) are recognized for their broad physiological activities, including significant antioxidant, antimicrobial, and gut microbiota-regulating effects. However, their limited bioavailability in biological systems restricts the full realization of these potentials. In order to improve the bioavailability of PPA, this paper established and optimized the preparation process of W/O/W purple potato anthocyanin nanoparticles (PPA-NPs). Based on the determination of the metabolites of PPA-NPs, in vivo experiments were conducted in rats to investigate the absorption and metabolism, antioxidant activity, and the impact on the intestinal microbiota of PPA-NPs. UPLC-Q-TOF-MSMS analysis showed that the absorption of anthocyanins was increased by 220.36% in rats gavaged with PPA-NPs compared to rats gavaged with PPA directly. Subsequent in vivo experiments revealed that PPA-NPs significantly bolster primary antioxidant markers, evidenced by elevated glutathione and superoxide dismutase levels and reduced malondialdehyde content. Moreover, PPA-NPs were found to positively alter the gut microbiome structure in aged rats, notably increasing the abundance of beneficial bacteria, such as Lactobacillus and Rothia, and improving microbial diversity. These findings suggest that W/O/W PPA-NPs markedly improve the bioavailability of PPAs, showcasing promising antioxidant properties and potential health benefits for gut health in vivo. Overall, this research presents a novel approach for developing nanodelivery systems aimed at enhancing the bioavailability of water-soluble substances.