Anthocyanins in plants are novel food ingredients with coloring, flavoring, and health-promoting effects. However, anthocyanins are susceptible to hydrolysis or sugar-group removal/ring-opening reactions by external factors, leading to loss of color, deterioration of flavor quality, and loss of bioactivity in foods. Studies have shown that under natural biological conditions, the structural stability of plant anthocyanin molecules is maintained via copigmentation of the various chemical components (polyphenols, alkaloids, nucleotides, metal ions, etc.) inside plants, resulting in the stabilization of color, flavor and nutritional value of anthocyanin foods. Therefore, mimicking the copigmentation effect of plant anthocyanins has become an important part of functional pigment research. This study showed the molecular copigmentation in anthocyanins, and focused on the latest progress in the stabilization of anthocyanins based on molecular copigmentation during preparation as well as the related applications in food processing, providing a basis and reference for the stabilization of natural anthocyanins in food processing.