In this study, chromatographic and mass spectrometry conditions, sample cleanup and extraction, composition and ratio of salt and purifiers were optimized, which established a high-throughput screening method for 11 plant growth regulators and 79 antibiotic drugs in sprout vegetables by ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Samples were extracted by 1% acetonitrile-EDTA-mcllvaine buffer solution, purified by QuEChERS, and separated by ACQUITY UPLC HSS T3 column with gradient elution. Electrospray positive and negative ion mode was used in multi-reaction monitoring mode, and matrix curve external standard method was used to quantify. The limits of quantitation of 90 compounds were in the range of 0.1~15.4 μg/kg. The average recoveries were in the range of 42.2%~138.6% with relative standard deviations lower than 17.2%. In this study, simultaneous, rapid and high-throughput screening and detection of 90 high-risk substances in sprout vegetables were established, which is conducive to a more full understanding of the quality and safety problems of sprout vegetables.