The aim of this study was to raise the quality control level of Scutellaria indica. A quick and stable Ultra Performance Liquid Chromatography (UPLC) method was established for the fingerprint analysis of Scutellaria indica. 32 common peaks were marked with 10 batches Scutellaria indica detected in 30 minutes using Similarity Evaluation System for Chromatographic Fingerprint of Traditional Chinese Medicine (2004A version). Besides, a high resolution mass spectrometer was used to identify flavonoids in Scutellaria indica. 27 flavonoids in Scutellaria indica were identified. And a series of fragmentation regularities were obtained, which could be used to the identification of the other flavonoids. Therefore, the established liquid chromatography tandem mass spectrometer (LC-MS) method could be successfully utilized to the quality control of Scutellaria indica.