Pesticide residues have been a focus of attention of food safety. Different varietal pakchoi plants grown in open fields were studied to understand effects of morphology, leaf wax content, and vitamin C on the deposition, dissipation, and metabolism of chlorothalonil. The loose pakchoi plants and flat leaves were conducive to pesticide deposition, but not plants with erect leaves. Chlorothalonil on nine varieties of pakchoi dissipated in the first-order kinetic with T1/2s of 1.4 ~ 2.0days. Vitamin C in pakchoi could promote the dissipation of chlorothalonil. Carbendazim could significantly promote the dissipation of chlorothalonil on pakchoi. Interestingly, four metabolites of chlorothalonil were identified in the pakchoi and the metabolic pathway was predicted by DFT calculations. The risk assessment showed that pakchoi were safe for consumption after 10days of application of the recommended dose. This work provides important information for the understanding of deposition, dissipation, and metabolism of chlorothalonil in pakchoi.