Plant polyphenols, especially their flavonoid subclass are important bioactive compounds. Simultaneous determination of total flavonoids (TFs) and total polyphenols (TPs) is crucial for studying the distribution characteristics of polyphenols. Traditional methods for determining TFs and TPs require complicated operational procedures, and reported flow injection analysis (FIA) methods have also been limited due to inefficiencies caused by carrier changing and system resetting. Simultaneous determination of TFs and TPs is difficult to achieve with the existing methods. Therefore, in this study, a merging-zone FIA technique was developed for the simultaneous determination of TFs and TPs based on the study of the AlCl3 and Folin-Ciocalteu colorimetric reaction mechanisms. The FIA parameters were optimized by univariate experimental design, and standard curves for TFs and TPs were established in the concentration ranges of 10-800 mg/L and 15-400 mg/L, respectively. The limit of detection of the proposed FIA method for TFs and TPs was 3.114 mg/L and 4.166 mg/L, and the limit of quantitation was 10.38 mg/L and 13.89 mg/L. The relative standard deviations were below 2.5% (n=15). The recoveries of spiked sample ranged from 93.89% to 103.8%, and the sample throughput was approximately 67 h-1. The proposed method was successfully applied to the simultaneous determination of TFs and TPs in nine plants, and the analytical results were in good agreement with those of traditional methods. This study provides a rapid, automated and reliable method for simultaneous quantitative analysis, showing high application potential for simultaneous evaluation of these two bioactive compounds in various plants.