The invention discloses a method used for separating and identifying flavonoid matters in tobacco by adopting liquid chromatography-mass spectrography. The method comprises the following steps: a sample is ground and dried, an extractant is added according to the standard that 0.1 ml of the extractant is added into 1 mg of the sample for extraction and centrifugation, a supernatant liquor is collected, water and chloroform are added according to the standard that 0.5 ml of the water and 1 ml of the chloroform are added into 1 ml of the supernatant liquor for centrifugation, and the supernatant liquor is collected for analysis; 153+ and 151- are adopted as characteristic ions for scanning, parent ions are extracted for second level mass spectrum scanning, and an obtained spectrogram is compared with a spectral library to determine a chemical structure and verified through a reference substance; the molecules and ions of the identified matters and myricetin, dihydromyricetin, catechinic acid / epicatechin, daidzein, glycitein and glycyrrhizin / isoliquiritigenin are adopted as characteristic ions for scanning, the molecules and ions of the searched glycosylation flavonoid matters are used as the parent ions for the second level mass spectrum scanning, an obtained spectrogram is compared with the spectral library to determine a chemical structure and verified through the reference substance. According to the invention, the method is suitable for the analyzing and detecting micro even trace flavonoid matters.