A rapid and simple method has been developed for the screening and identification of natural antioxidants of Flos Lonicerae Japonicae (FLJ), derived from the flower buds of Lonicera japonica. The hypothesis is that upon reaction with 1,1-diphenyl-2-picrylhydrazyl (DPPH), the peak areas (PAs) of compounds with potential antioxidant effects in the HPLC chromatograms will be significantly reduced or disappeared, and the identity confirmation could be achieved by HPLC-DAD-TOF/MS hyphenated technique. Using the proposed approach, about 14 compounds in the FLJ extract were found to possess a potential antioxidant activity. They were identified as chlorogenic acid (1), 1-O-caffeoylquinic acid (1-O-CQA, 2), caffeic acid (4), 4-O-CQA (5), rutin (7), isoquercitrin (8), luteolin-7-O-glucoside (9), lonicerin (10), 4,5-O-dicaffeoylquinic acid (4,5-O-diCQA, 11), 3,5-O-diCQA (12), 1,3-O-diCQA (13), 3,4-O-diCQA (14), 1,4-O-diCQA (16), and luteolin (17). In addition, the free radical scavenging capacities of the available identified compounds were also investigated by HPLC assay. The results indicated that the compounds with PAs significantly decreasing were natural antioxidants, whereas those with PAs not changing presented no activities, which accordingly indicated that this newly proposed method could be widely applied for rapid screening and identification of natural antioxidants from complex matrices including Chinese herbal medicines.