SiJunZiTang (SJZT), a classic Traditional Chinese Formula (TCMF) consisting of four herbs, Radix Ginseng, Atractylodes macrocephala, Poria cocos and Glycyrrhiza uralensis, has been demonstrated to show protective effects on intestine and stomach injure. The chromatographic quality control is needed. UPLC–Q-TOF-MS is a rapid and efficient technique for analysis of complex sample in combination with UPLC and tandem mass spectrometry (MS/MS). In this paper, UPLC–MS fingerprinting of SJZT was developed. As a result, 66 compounds including ginsenosides, flavonoids, triterpenoid and coumarins were detected, 58 of them were tentatively identified. The major constituents of SJZT were ginsenosides and flavonoids that coming from Radix Ginseng and Glycyrrhiza uralensis.