Chrysanthemum is an important traditional Chinese medicine and is drunk daily as a herbal tea. Chlorogenic acids and flavonoids are generally considered as the bioactive compounds. In this work, six kinds of Juhua Tea were analyzed and their active compounds and antioxidant activities were compared. In total, 32 phenolic compounds were profiled and identified using HPLC-DAD/ESI-MSn, composed of chlorogenic acids (10), flavones (8), chalcones (8), flavanones (4) and flavonols (2). Chalcones were the main flavonoids in Kunlun Xueju (Coreopsis tinctoria) extract, while flavones and chlorogenic acids were dominant in the five Chrysanthemum teas. Total chlorogenic acids content (TCA) was highest in Tai Ju (Chrysanthemum morifolium cv. 'Tai Ju') (8.59 ± 0.87 mg/g DW), and total flavonoids content (TF) was highest in Kunlun Xueju (87.2 ± 7.0 mg/g DW), which were both lowest in Ganye Ju (Chrysanthemum eticuspe) (TCA 0.86 ± 0.26 mg/g DW, TF 1.43 ± 0.41 mg/g DW). Huangin Ju (Anthemis tinctoria) possessed the most flavones (19.7 ± 0.6 mg/g DW). Antioxidant capacity of each drink, assessed by Folin-Ciocalteu, DPPH, ABTS and FRAP assays, consistently showed that Kunlun Xueju extract possessed stronger antioxidant activity than the other five, suggesting that the flavonoids content accounted for the free radical scavenging. The present work provides a method for the characterization and quality control of Juhua Tea. Moreover, it is a guideline for consuming choice, due to the different biological functions resulting from chalcones, chlorogenic acids, and flavones.