Objective To control the quality of Evodia rutaecarpa better. Methods An HPLC-DAD-MS/MS method was established for the rapid and efficient identification of bioactive constituents and for simultaneous quantitative analysis of four bioactive ingredients including evodiamine, rutaecarpine, dehydroevodiamine, and evodin in E.rutaecarpa, which was applied to evaluating eight samples of E. rutaecarpa and its varieties from different areas.Results Thirteen potentially bioactive constituents including one flavonoid glycoside, one limonin, four indoloquinazoline alkaloids, and seven quinolone alkaloids were identified in all samples and the contents of dehydroevodiamine, evodine, evodiamine, and rutaecarpine varied widely from 0.10% to 0.51%, 0.49% to 3.12%,0.07% to 1.56%, and 0.10% to 0.69%, respectively. Conclusion This method is found to be convenient, fast,accurate, and it is facilitated to improve the quality control standard of E. rutaecarpa and related products.