Anthocyanins are key pigments responsible for apple fruit coloration, influencing not only its appearance and marketability but also contributing significantly to its nutritional and health benefits. In their natural state, anthocyanins are chemically unstable. However, glycosylation modifies them into anthocyanin derivatives known as anthocyanin glycosides, which exhibit markedly enhanced stability and improved water solubility. As a result, most naturally occurring anthocyanins exist in the form of anthocyanin glycosides. The biosynthesis of anthocyanins involves a series of structural genes within the phenylpropanoid and flavonoid pathways (including PAL, C4H, 4CL, CHS, CHI, F3H, DFR, ANS/LDOX, and UFGT). The MYB–bHLH–WD40 transcriptional complex serves as the core regulatory mechanism controlling anthocyanin synthesis, with additional transcription factors also playing important roles. This review systematically summarizes recent advances in the structural characteristics, biosynthetic pathways, molecular regulatory mechanisms, and environmental factors affecting anthocyanin accumulation in apples. These insights are important both for consumer health and for breeding apple cultivars with enhanced anthocyanin content.