Functional ingredients have multiple health benefits for humans, but are sensitive to oxidative degradation during manufacture and storage, and have poor chemical stability and reduced bioaccessibility. Therefore, microcapsules are prepared by encapsulating the active ingredient in a matrix to enhance the stability of the active ingredient. Their use as microcapsule carriers in the food industry is now an effective and promising technology. This paper reviews the preparation of microcapsules based on different principles. It summarizes the protein and polysaccharide bioactive substances commonly used for encapsulation. It also discusses the practice of modifying the wall material by chemical reactions (Maillard reaction) to obtain excellent properties. Finally, the applications of microcapsules in the production of beverages, baked goods, meat, dairy products, probiotic delivery and food preservation are discussed as well as their feasibility as effective protective bioactive substance delivery systems. The microencapsulation process can improve the storability of food products, make bioactive compounds stable over time and apply co-microencapsulation in the formulation of co-effective functional foods, which is a direction for future research.