This paper developed a rapid method using near infrared spectroscopy (NIRS) to differentiate two species of cortex phellodendri (CP), cortex phellodendri chinensis (PCS) and cortex phellodendri amurensis (PAR), and to predict quantitatively the content of berberine and total alkaloid content in all cortex phellodendri samples. Three alkaloids, berberine, jatrorrhizine and palmatine were analyzed simultaneously with a Thermo ODS Hypersil column by gradient elution with a new mobile phase under high-performance liquid chromatography-diode array detection (HPLC-DAD). Berberine content determined by HPLC-DAD was exploited as a critical parameter for successful discrimination between them. Multiplicative scatter correction (MSC), second derivative and Savitsky-Golay (S.G.) were utilized together to correct the scattering effect and eliminate the baseline shift in all near infrared diffuse reflectance spectra as well as to enhance spectral features in order to give a better correlation with the results obtained by HPLC-DAD. With the use of principal component analysis (PCA), samples datasets were separated successfully into two different clusters corresponding to two species. Furthermore, a partial least squares (PLS) regression method was built on the correlation model. The results showed that the correlation coefficients of the prediction models were R=0.996 for the berberine and R=0.994 for total alkaloid content. The influences of water absorption bands present in the NIR spectra on the models were also investigated in order to explore the practicability of NIRS in routine use. The outcome showed that NIRS possibly acts as routine screening in the quality control of Chinese herbal medicine.