The analysis of pesticide residues in aquatic products is challenging due to low residue levels and the complex matrix interference. In this study, we developed a simple, fast method for the trace analysis of 90 pesticides and metabolites in aquatic products. The analytes covered a wide polarity range with log Kow (log octanol-water partition coefficient) ranging from −1.2 to 6.37. Grass carp (Ctenopharyngodon idellus) and prawn (Penaeus chinensis) samples were chosen to validate the quantification method. The samples were extracted by 0.2% formic-acetonitrile, cleaned by solid-phase extraction (PRiME HLB), and analyzed by high performance liquid chromatography−tandem mass spectrometry. The results showed good linearities for the analytes and were observed in the range of 0.05–50 μg/L. The recoveries of the method were within 50.4–118.6%, with the relative standard deviations being lower than 20%. The limits of quantifications (LOQs) of the method were in the range of 0.05–5.0 μg/kg, which were superior to values compared with other research. The developed method was applied to detect pesticide residues in prawn samples from eastern coastal areas of China. Three herbicide residues of diuron, prometryn, and atrazine were detected in prawn samples. The method was sensitive and efficient, which is of significance in expanding the screening scope and improving the quantitative analysis efficiency in aquatic products.