The aim of this study was to raise the quality control level of Scutellaria indica. A quick and stable ultra performance liquid chromatography method was established for the fingerprint analysis of S. indica. A total of 32 common peaks were marked with 10 batches S. indica detected in 30 min 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 S. indica. A total of 27 flavonoids in S. indica were identified. And a series of fragmentation regularities were obtained, which could be used for the identification of other flavonoids. Therefore, the established liquid chromatography–tandem mass spectrometer method could be successfully utilized for the quality control of S. indica.