A rapid and nondestructive near infrared spectroscopy (NIRS) was used to differentiate different geographical Paeoniae Radix and quantitatively predict the content of main active components. Paeoniflorin, albiflorin and benzoylalbiflorin were analyzed simultaneously with an Agilent Zorbax SB-C 18 column by gradient elution under high-performance liquid chromatography-UV detection (HPLC-UV). Multiplicative scatter correction (MSC), first derivative and Savitsky-Golay were utilized together to correct the scattering effect and eliminate the baseline shift in all near infrared diffuse reflectance spectra in order to give a better correlation with the results obtained by HPLC-UV. Multiplicative regression methods were discussed. The spectra calibration equations produced highest correlation coefficient values (R 2 ) and lowest root mean square error of prediction (RMSEP) were used for the determination of paeoniflorin, albiflorin and benzoylalbiflorin. The RMSEP of paeoniflorin, albiflorin and benzoylabiflorin were 0.866 mg/g, 0.369 mg/g and 0.084 mg/g, respectively, and the R 2 of cross validation were 0.986, 0.939 and 0.971, respectively. Furthermore with the use of principle component analysis (PCA), Paeoniae Radix was clustered according to different cultivation area. The results indicated that the NIRS method could be used for the quality control of Chinese herbal medicine.