The objective of the present study was to develop a method for rapid determination of baicalin and total flavonoids in radix scutellariae by near infrared diffuse reflectance spectroscopy.　Sixty one samples of radix scutellariae from different areas containing baicalin of 12.24%-21.34% and total flavonoids of 16.08%-26.52% were used. The range of 8 000-4 000　cm-1 of near infrared spectra (NIRS) was selected. Calibration models were established using the PLS(partial least squares). Different spectra pretreatment methods were compared and the optimal model was selected. The study showed that first derivative pretreatments and minimum-maximum normalization methods can be used to extracted spectra information thoroughly to analyze the contents of baicalin and total flavonoids, respectively.The correlation coefficient (r)of baicalin was 0.902　4， SEC was 1.01(standard deviation of the calibration sets) and SEP was 0.876　4(standarddeviation ofthe prediction sets).　The correlation coefficient(r) of total flavonoids was 0.952　7， SEC was 0.785　0 and SEP was 0.521　1. Results indicated that near infrared diffuse reflectance spectroscopy method can be used to analyze the main active components in radix scutellariae rapidly.