Objective To quantify the contents of baicalin, wogonoside, baicalein, wogonin, chrysim and oroxylinA in the Scutellaria baicalensis Georgi with different storage time by liquid chromatography-mass spectrometry( LC-MS) and determine the stability of Scutellaria baicalensis Georgi. Methods The LC system consisted of an Agilent Zorbax XDB-C18 column (2. 1 mm×150 mm,3. 5 μm) with acetonitrile and water (0. 1% formic acid) in linear gradient condition. The flow rate was 0. 2 mL·min-1 and the wavelength of detection was 276 nm. The mass spectrometer was operated under the positive ion mode with the ESI source. The precursor-to-product ion pair was 447/271 for baicalin,461/285 for wogonoside,271/123 for baicalein, 285/270 for wogonin, 255/153 for chrysim and 285/270 for oroxylinA, respectively. Results The contents of baicalin, wogonoside, baicalein, wogonin, chrysim and oroxylin A had a linear relationship with their peak areas within the ranges of 8. 86-177. 2, 2. 33-46. 5, 2. 6-52. 0, 0. 52-10. 4, 0. 04-0. 8 and 0. 04-0. 8 μg · mL-1 , respectively. The contents of baicalin, wogonoside, baicalein, wogonin, chrysim, and oroxylin A were overall decreased over the first 3 months of storage,but remained relatively stable between 0 and 18 months. Conclusion The results provides basis for the establishment of quality standard.