Puerarin (PUE) and daidzein (DAI) are polyphenols with extensive biological activities. In the present study, the interactions between PUE/DAI and micellar casein (MC) were investigated, and the physicochemical properties of their complexes were analyzed. The results of fluorescence spectrum analysis and molecular docking revealed that the main interactions between DAI and MC were hydrophobic forces, while that between PUE and MC was hydrogen bonding. The FTIR and XRD analyses confirmed the formation of complexes between MC and PUE/DAI. After binding to PUE/DAI, the size of MC increased. The weight loss rate of MC decreased after complexing with PUE/DAI, but its morphology was not extensively modified. The DPPH radical scavenging capacities of PUE-MC and DAI-MC complexes were higher than those of free PUE/DAI in both water and ethanol. In vitro release experiments showed that the release rate of PUE/DAI was inhibited by MC under simulated intestinal conditions. PRACTICAL APPLICATIONS: The low water solubility and poor bioavailability of PUE and DAI limit their application. Micellar casein has high affinity for PUE and DAI. After encapsulated by micellar casein, the release rates of PUE and DAI were prolonged during simulated intestinal digestion. The results would provide useful information for improving the solubility and bioavailability of PUE and DAI, and broadening the use of them in the food and pharmaceutical industry.