Anthocyanins are natural pigments produced during plant secondary metabolism and have various biological activities and provide benefits to human health. However, the structure of anthocyanins is easily affected by environmental factors. By employing microencapsulation technology and polysaccharides, proteins, and other materials as wall components, anthocyanin can be encapsulated to enhance their stability, impart controlled-release properties, and further enhance their biological activity. This review provides an overview of the molecular structure and biological activity of anthocyanins, as well as the challenges of their application in the food industry. Based on carrier materials and packaging strategies, the microencapsulation technology of anthocyanins has been summarized. Additionally, this review summarizes the current applications and future trends of anthocyanin microcapsules in the food industry, particularly in food additives and food intelligent packaging. The aim of this review is to provide reference for the development of high-value anthocyanin microcapsule products.