•Twelve main phenolic compounds (PC) were identified in different rice varieties.•Bran and husk provide more than 90% of PC and antioxidant activity of whole rice.•Ferulic acid, gallic acid and protocatechuic acid were the highest 3 PCs in rice bran.•P-Hydroxybenzaldehyde was the main PC existed in rice husk (14.46–23.72 μg·g−1).•Japonica rice has significant higher PC and antioxidant activity than Indica rice. Utilization of phenolic compounds in rice husk and bran is important for improving the functionality of rice by-products. Eight rice varieties planted in different area were selected to analyze the phenolic compounds distribution of fractions in Japonica and Indica rice by using UPLC-MS method. A total of 12 phenolic compounds were identified in all rice varieties. Ferulic acid, gallic acid, protocatechuic acid and syringic acid were the dominant phenolic compounds in rice bran, while p-Hydroxybenzaldehyde was the main phenolic compounds existed in rice husk (14.46–23.72 µg·g−1). Bran and husk fractions provide more than 90% of phenolic compounds and antioxidant activity of whole rice. Regardless of the planting environmental effects, Japonica rice has significant higher phenolic compounds and antioxidant activity than Indica rice (P < 0.05). Therefore, it can be concluded that the distribution of phenolic compounds were strongly correlated with the rice varieties and fractions.