In food science, the application of bioactive compounds is promising, but the deficiencies in their solubility, stability, and bioavailability seriously limit their efficacy. Co-delivery can control the release of bioactive substances and achieve synergistic effects to enhance efficacy. For this reason, co-delivery systems have emerged as a novel strategy that has attracted much attention from researchers in recent years. This review provides an in-depth analysis of the unique properties of different bioactive ingredients and systematically describes the latest research progress of co-encapsulation systems such as emulsions, nanoparticles, and liposomes. It also introduces their advanced characterization tools. Meanwhile, the kinetic law of the release of bioactive ingredients in vivo and its molecular mechanism are discussed in depth through experimental data and theoretical analysis. In addition, the potential application value of the co-encapsulation system in the food industry is also introduced in detail. In summary, this study not only provides a solid theoretical foundation and rich reference basis for further research in the field of co-encapsulation, but also provides new ideas and directions to promote the construction and development of rational and efficient co-encapsulation systems, and to promote the innovation and development of functional foods and precision nutrition.