Pesticide residues in foodstuffs can lead to several undesirable effects. A simple and high-throughput targeted screening method analyzing multi-residue pesticide in aquaculture water based on ultra-high-performance liquid chromatography-Q/Orbitrap mass spectrometry (UHPLC-Q/Orbi MS) was developed and validated. In this technique, the peaks of the compound using precursor ions were recorded by the full scan, which was used for rough quantitative analysis with single point matrix matched calibration. The qualitative identification was performed following the stringent confirmation criteria with fragment ions, retention time, and an isotopic pattern. Additionally, solid-phase extraction with an HLB (Hydrophilic/Lipophilic Balanced) column was selected to enrich and separate target pesticides from water. The screening detection limit of 33 compounds are less than 2 ng·L−1, while 26 compounds range from 2 ng·L−1 to 10 ng·L−1, 19 compounds are at the range of 10–200 ng·L−1, and the other two compounds are 200 ng·L−1 and 1000 ng·L−1. Most of the recovery results were found to be between 60~130%. Finally, the method was successfully applied to the analysis of pesticide residues in 30 water samples from aquaculture environment in Shanghai, indicating its applicability in pesticide screening for environmental monitoring.