In order to optimize anthocyanin purification process, comparing the yield and antioxidant activity of anthocyanin in rice grain and husk among different black rice varieties, a single factor experiment design was used to investigated the effect of various factors of resin adsorption in the purification of black rice anthocyanin; Then, the yield of purified anthocyanin of black rice and husk in different varieties was compared; Finally, the antioxidant activity of anthocyanin from different varieties was compared by 1, 1-diphenyl -2- trinitrophenylhydrazine (DPPH) method. The results showed that the optimum purification condition for anthocyanin was 4 h of static adsorption equilibrium, 1.5 h of the desorption time, 2.5 of pH, 30℃ of temperature, 70% ethanol of eluent. The highest yield of anthocyanin in grain came from Fuheixiangnuo (21.3 mg/100 g), however, to husk from Guchengheinuo (22.6 mg/100 g). Meanwhile, Guchengheinuo possessed the highest total yield of anthocyanin, 43.2 mg/100 g. The antioxidant capacity of anthocyanin from husk increased by 13.9% compared with that from grain. In the identification of the key genes of anthocyanin synthesis pathway of black rice varieties, it was found that there was no flavonoid -3 "-hydrogenase gene (OsF3 "H) in Aixuenuo and its anthocyanin yield in rice husk was also the lowest. These findings have more theoretical significance in enhancing the comprehensive utilization value of black rice varieties.