Cardiovascular disease (CVD) is a group of diseases affecting the heart and blood vessels and is the leading cause of morbidity and mortality worldwide. Increasingly more evidence has shown that the senescence of vascular endothelial cells is the key to endothelial dysfunction and cardiovascular diseases. Anthocyanin is a type of water-soluble polyphenol pigment and secondary metabolite of plant-based food widely existing in fruits and vegetables. The gut microbiome is involved in the metabolism of anthocyanins and mediates the biological activities of anthocyanins and their metabolites, while anthocyanins also regulate the growth of specific bacteria in the microbiota and promote the proliferation of healthy anaerobic flora. Accumulating studies have shown that anthocyanins have antioxidant, anti-inflammatory, and anti-aging effects. Many animal and in vitro experiments have also proven that anthocyanins have protective effects on cardiovascular-disease-related dysfunction. However, the molecular mechanism of anthocyanin in eliminating aging endothelial cells and preventing cardiovascular diseases is very complex and is not fully understood. In this systematic review, we summarize the metabolism and activities of anthocyanins, as well as their effects on scavenging senescent cells and cardioprotection.