Lycium ruthenicum is a therapeutic plant and its fruits (black goji) are commonly used as a traditional Chinese medicine. This review comprehensively discusses the recent research developments of black goji anthocyanins (BGAs), including chemical compositions, biosynthesis, color properties and health benefits. Among the 39 identified BGAs, most are 3,5-diglycoside derivatives of petunidin (>95%) with an individual anthocyanin [petunidin 3-O-rutinoside (trans-p-coumaroyl)-5-O-glucoside], accounting for 80% of the total BGAs. Due to their unique anthocyanin profile, BGAs possess various health benefits, including antioxidant activities, α-glucosidase inhibiting activity, alleviating insulin resistance, improving mitochondrial function, anti-inflammatory effects, etc., and therefore have the potential to treat a range of chronic diseases, such as type 2 diabetes mellitus, memory disorders, stroke, colitis, atherosclerosis, cardiovascular and cerebrovascular diseases. In addition, BGAs exhibit a pH-dependent “red-purple-blue” pattern of color change and thus could be used as natural colorants and to prepare smart food packaging materials. This review is valuable for broad applications of BGAs as promising natural colorants, functional foods and potential herbal medicines.