A rapid procedure for the determination of 482 pesticide residues in Chinese Materia Medica by GC-Q-TOF/MS and LC-Q-TOF/MS (379 pesticides for LC, 327 pesticides for GC, and 226 pesticides for both) was developed. Radix codonopsis was chosen as the matrix for verification, and a comparative study on the QuEChERS sample preparation was carried out, between a fully automated workstation and manual operation, in terms of limits of quantitation, recovery rate and RSD at 3 spiked levels of 10 μg kg-1, 20 μg kg-1 and 100 μg kg-1. In the linear range of each pesticide in a concentration range of 5-100 μg L-1, the linear correlation coefficients R2 of 85% of the pesticides for GC and 88% for LC were equal to or greater than 0.990. Taking recovery 70-120% and RSD ≤ 20% as the satisfactory standard, the automated workstation performed better at 10 μg kg-1 and 20 μg kg-1 than manual operation, and the numbers of satisfactory pesticides of GC & LC were 401 and 418 for the automated approach, and 378 and 400 for manual, while the two approaches were almost even at 100 μg kg-1, 421 vs. 424. Besides, the automated workstation presented lower RSD (more pesticides ≤10%) and better recovery quality (more pesticides within 90-110%). Following the method verification, 50 Radix codonopsis samples purchased from local markets were prepared with the automated workstation and analyzed by GC and LC-Q-TOF/MS. 18 pesticides were detected in 38 samples, one of which was a highly toxic pesticide. The automated QuEChERS workstation can handle 40 samples in one cycle within 6 hours, and realize whole-process automation covering from samples after "weighing" to "injection into vials". The batch-to-batch, day-to-day, and lab-to-lab consistency and 24 × 7 workability of the automated solution have demonstrated a promising and ideal replacement for manual operation in sample preparation.