Anthocyanins play an important role in the colour of red wine or mulberry wine. The effect of anthocyanin structures (substitution therein) on the self-association and colour in an aqueous alcohol solution was investigated in order to provide helpful knowledge about the relationship between anthocyanin structure and colour. The addition of hydroxyl at the C3′ position weakens self-association, whereas addition at the C5′ position facilitates self-association. However, the hydroxyl substitutions at the C3′ and C5′ positions enhance colour. The methoxy substitutions at the C3′ and C5′ positions enhance the self-association and the colour. The replacement of glucoside with the disaccharide rutinoside at the C3 position was detrimental to self-association, but the substitution of rutinoside at the C3 position produced a stronger colour than the substitution of glucoside at the same position. Cyanidin 3-O-glucoside and cyanidin 3-O-rutinoside enhanced colour via intramolecular co-pigmentation instead of self-association. The anthocyanin colour was affected synthetically by the types and positions of the substituent in the anthocyanin molecule.