Murraya exotica L. is one of the two official source species of traditional Chinese medicine Murrayae Folium et Cacumen. At present, a rapid HPLC analysis method to simultaneously determine two major coumarins, hainanmurpanin (1) and meranzin (2), and one main flavonoid,3,5,6,7,3′,4′,5′-heptamethoxyflavone (3), from the leaves and twigs of M. exotica was established. The analysis was performed on a DIKMA Spursil C18 column (4.6 mm×250 mm, 5 µm) at a flow rate of 1 mL/min, using acetonitrile–H2O (5:5, v/v) as mobile phase. The column temperature was 25 ºC, and the detected wavelength was at 320 nm. The three analytes (1–3) were separated well with good linearity, precision, stability and repeatability. The average recoveries were in the range of 100.52%–101.97%, with RSD less than 1.73%. Twenty batches of M. exotica from different habitats were detected, and the sum of the contents of 1–3 was in the range of 1.55–7.45 mg/g, respectively. Besides, the contents of these three analytes were also determined for the samples from different medicinal parts (stems, lateral branches, mixture of twigs and leaves) and different harvest times. The results showed that the contents of these three analytes in leaves and twigs are much higher than those in the stems or lateral branches; the plants harvested from June or October contain more active compoundsthan those from the other months. The above results proved that this high performance and simple HPLC assay can be readily utilized as a practical method for the quality control of M. exotica.