A total of 50 commercial samples of Aurantii Fructus, originating from Poncitrus trifoliata for Aurantii Fructus Immaturus, Citrus aurantium, and C. wilsonii for Aurantii Fructus Maturus, respectively, were collected from Taiwan and China herbal markets. Contents of the constituents in the samples were determined within 60 min using a developed HPLC method, which had been validated in terms of precision, repeatability, and accuracy. The results of the analyses showed that the constituents were closely related to the species and also the degree of maturity of the fruits, especially in the case of hesperidin (HE), naringin (NG), neohesperidin (NE), naringenin-7-glucoside (NGC), narirutin (NR), and quercetin (QU). The mature fruits (C. aurantium and C. wilsonii) contained chiefly NG, HE, and NE and the immature ones (P. trifoliata) had NG, NR, and QU majorly. Within the mature samples, the ratios of HE/NE and NGC/NE values were higher than 2.94 and 0.21 in C. aurantium and lower than 1.31 and 0.02 in C. wilsonii, respectively. A flowchart that is useful for identifying Aurantii Fractus was devised, based on the various chemical identification methods.