A precise analytical method was established for rapid screening of 49 antibiotic residues in aquatic products by ultra-high performance liquid chromatography-quadrupole time of flight mass spectrometry (UPLC-QToFMS). The quick, easy, cheap, effective, rugged and safe (QuEChERS) process was refined for effective sample preparation. The homogenized samples of aquatic products were extracted with 3% acetic acid in acetonitrile, salted out with anhydrous magnesium sulfate and sodium chloride, and cleaned up by octadecylsilane (C18) and primary-secondary amine (PSA) powder. Then, the purified samples were separated on a BEH C18 column using 0.1% formic acid and methanol as mobile phases by gradient elution, detected by MS under positive Electron Spray Ionization (ESI+) mode. The linear range of matrix-matched calibration curve was 1–100 μg/L for each compound with the correlation coefficients in the range of 0.9851–0.9999. The recoveries of target antibiotics at the different spiked levels ranged from 60.2% to 117.9% except for lincomycin hydrochloride, whereas relative standard deviations (RSDs) were between 1.6% and 14.0% except for sulfaguanidine in grass Carp, Penaeus vannamei and Scylla serrata matrices. The limits of detection (LODs) (S/N = 3) for the analytes were 0.05–2.40 μg/kg, 0.08–2.00 μg/kg and 0.10–2.27 μg/kg and the limits of quantification (LOQs) (S/N = 10) were 0.16–8.00 μg/kg, 0.25–6.66 μg/kg and 0.32–7.56 μg/kg in grass Carp, Penaeus vannamei and Scylla serrata, respectively. The method was successfully applied to grass Carp, Penaeus vannamei and Scylla serrata, demonstrating its ability for the determination of multi-categories antibiotic residues in aquatic products.