The safety of traditional Chinese medicine (TCM) has garnered considerable interest worldwide. In this study, a high-throughput method for the determination of 255 pesticide residues in decoctions of Radix Codonopsis and Angelica sinensis was developed using liquid chromatography-time-of-flight/mass spectrometry. The methodological verification demonstrated the accuracy and reliability of this method. The frequently detected pesticides in Radix Codonopsis and Angelica sinensis were determined to build a correlation between pesticide properties and the transfer rate of pesticide residues in their decoctions. Water solubility (WS) with a higher correlation coefficient (R) made a significant contribution to the accuracy of the transfer rate prediction model. The regression equations for Radix Codonopsis and Angelica sinensis were T = 13.64 log WS + 10.56 with a correlation coefficient (R) of 0.8617 and T = 10.66 log WS + 25.48 with a correlation coefficient (R) of 0.8072, respectively. This study provides preliminary data on the potential risk of exposure to pesticide residues in Radix Codonopsis and Angelica sinensis decoctions. Furthermore, as a case study on root TCM, this approach may serve as a model for other TCMs.