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In this paper, the three active components in Scutellaria Extract were rapidly determinate by near-infrared reflectance spectroscopy (NIRS). 100 samples of Scutellaria Extract from 12 different pharmaceutical factories were divided into a calibration set (80 samples) and a validation set (20 samples). In combination with the practical least square (PLS), the quantitative calibration models were established, involving baicalin, baicalein and wogonin. The correlation coefficient of cross-validation (R2cv) was 0.99481, 0.99867 and 0.99484 for baicalin, baicalein and wogonin, the root-mean-square error of calibration (RMSEC) was 0.440, 0.0225 and 0.0111, the root-mean-square error of cross-validation (RMSECV) was 2.259, 0.0553 and 0.0483. The validation samples were used to evaluate the performance of the models, the correlation coefficient of prediction (r2) was 0.9882, 0.9965 and 0.9909, the root-mean-square error of prediction (RMSEP) was 0.486, 0.0271 and 0.0110. The results indicated that NIRS can provide a simple and accurate way in the determination of the baicalin, baicalein and wogonin content in Scutellaria Extract.