A simple, sensitive and accurate HPLC-DAD method was developed for simultaneous determination of wuchuyuamide-I, quercetin, limonin, evodiamine and rutaecarpine in Evodia rutaecarpa that has been widely used as one of the traditional Chinese medicines (TCMs). Chromatographic separations were performed on a reverse-phase C18 column with the gradient elution of acetonitrile–water and the simultaneous detection at five wavelengths. Good linear behaviors over the investigated concentration ranges were observed with the values of r higher than 0.999 for all the analytes. The recoveries measured at three levels varied from 98.77 to 102.36%. The validated method was successfully applied for the simultaneous determination of the five chemical constituents in 36 batches of samples collected from different regions or time that were investigated and authenticated as E. rutaecarpa (Juss.) Benth. Hierarchical clustering analysis (HCA) and principal components analysis (PCA) were performed to differentiate and classify the samples based on the contents of the five characteristic constituents. The total contents of evodiamine and rutaecarpine in different samples were calculated and the blending method proposed was demonstrated to be very useful in saving resources and in guiding rational herb use.