The screening and analysis of bioactive components in traditional Chinese medicines (TCMs) is very important not only for the quality control of Chinese herbs but also for elucidating the therapeutic principles. This study developed a new method for screening and analyzing bioactive compounds from TCMs using centrifugal ultrafiltration coupled with high-performance liquid chromatography. The method was successfully applied in the binding study of Flos Lonicerae Japonicae with bovine serum albumin (BSA), and 11 compounds were found to be bound with the BSA. Eight of them were positively identified as chlorogenic acid, caffeic acid, rutin, quercetin-3-O-glucoside, luteolin-7-O-glucoside, lonicerin, 3, 5-di-O-caffeoyl quinic acid and 3,4-di-O-caffeoyl quinic acid. Another three compounds were tentatively identified as two isomers of chlorogenic acid and one isomer of di-O-caffeoyl quinic acid by comparing the UV data and MS data with the previous reports. Based on modern pharmacological study, these compounds are the major bioactive components in Lonicera japonica. Therefore, the proposed method could be a good approach to predicting the potential bioactivities of multiple compounds in TCMs simultaneously.