A multi-class screening method for the determination of veterinary drugs and pesticides in eggs was developed by high performance liquid chromatography quadrupole-time-of-flight mass spectrometry (HPLC-QTOF-MS). A single-injection workflow was developed for qualitative analysis, and method validation was conducted in terms of retention time deviation (ΔRt), exact mass error (Δm), selectivity, specificity, precision and trueness. The characteristic fragment ions in information dependent acquisition (IDA) mode were summarized for retrospective and non-target screening. Five of 70 samples were found positive with sulfachloropyridazine, sulfamonomethoxine and fipronil sulfone. Compared with triple-quadrupole (QqQ) MS method, the obtained results showed that QTOF-MS gave comparable results to QqQ-MS with residue concentrations higher than 10 μg·kg−1, whereas QqQ-MS was more powerful at lower concentrations (<1 μg·kg−1). Moreover, the amount of fragment ions acquired by HPLC-QTOF-MS decreased substantially at trace levels, which may be a potential cause of reduced reliability of identification.