Many active ingredients in food products are destroyed by gastric acids and enzymes as they pass through the stomach, thereby reducing the desired effect of the target ingredient. In addition, traditional microcapsule preparation methods usually break up the dispersion by mechanical stirring or oscillation, which generates droplets of uneven size and inconsistent inclusion content, and mechanical external forces may cause denaturation and inactivation of active substances. This study aimed to use microfluidics to generate Oil-in-water-in-oil (O/W/O) droplet structures with good monodispersity and highly tunable properties, and to further prepare microcapsules with high encapsulation rate and targeted intestinal release by taking advantage of the cross-linking properties of alginate that reacts with Ca2+ under acidic conditions. Finally, the particle size distribution, release effect, encapsulation effect and oxidative stability of the core-shell microcapsules were evaluated. In this study, two types of microcapsules, homogeneous and core-shell microcapsules, were prepared by selecting tea polyphenols and vitamin E as models for hydrophilic and lipophilic bioactive compounds, respectively. Thin shell microcapsules with a shell thickness of about 25 μm were prepared using PDMS chip conditioning. Large microcapsules with a particle size of 230 μm were generated by using capillary glass tube chips, which had an excellent antioxidant property with a retention rate of 88.66 ± 1.25% of VE after 20 days of storage at 4 °C, while all of the VE was oxidized in the bare environment. In addition, in simulated gastric fluid, the release of VE was only about 20%, while in artificial intestinal fluid, the release was close to 100%, so the microcapsules also had intestinal targeting properties.