Numerous natural preparations in traditional Chinese medicine are prepared as decoctions. Processing factors (PFs) comparing the levels of pesticide residues in decoctions to those in the corresponding unprocessed products should be considered in exposure assessments. Thus, this study determined the residue levels of six pesticides (chlorpyrifos, phoxim, imidacloprid, thiamethoxam, fenpropathrin, and emamectin benzoate), as well as 3,5,6-trichloropyridinol, the primary metabolite of chlorpyrifos, and clothianidin, the main metabolite of thiamethoxam in Baishao, Paeoniae radix lactiflora (Fam. Ranunculaceae). The results showed that significant time-response effects were present for the release of pesticides from P. radix. The PFs calculated were < 1, indicating a significant reduction in pesticide residues after TCM processing. The water solubility and partition coefficient values of the pesticides may have played a basic role in the dissipation of the residues during the TCM decocting process. A risk assessment based on the hazard quotient with PFs revealed that exposure to pesticide residues in P. radix was far below the levels that might pose a health risk. In conclusion, the results presented here are of theoretical and practical value for the safety evaluation of TCMs.