This study investigated the phenolic compounds of 15 Chrysanthemum morifolium Ramat cv. ‘Hangbaiju’, including 6 ‘Duoju’ and 9 ‘Taiju’ using high performance liquid chromatography. The antioxidant activities of these ‘Hangbaiju’ were estimated by DPPH, ABTS and FPAR assays. Results showed that a total of 14 phenolic compounds were detected in these flowers, including 3 mono-caffeoylquinic acids, 3 di-caffeoylquinic acids, 1 phenolic acid and 7 flavonoids. ‘Duoju’ and ‘Taiju’ possessed different concentration of phenolic compounds, and ‘Taiju’ exhibited higher caffeoylquinic acids and stronger antioxidant activities than ‘Duoju’. Caffeoylquinic acids showed a strong correlation with the antioxidant activities of the samples. Principal component analysis revealed an obvious separation between ‘Duoju’ and ‘Taiju’ using phenolic compounds as variables. Apigenin-7-O-glucoside, 3,5-di-O-caffeoylquinic acid, luteolin and acacetin were found to be the key phenolic compounds to differentiate ‘Duoju’ from ‘Taiju’.