Dietary risk assessment generally combines food consumption data and the concentration of pesticide by using the risk quotient (RQ) method. Chlorothalonil is the second popular fungicide in the world, and its residue and risk assessment in water spinach remain unknown. In this paper, the field trials of chlorothalonil in water spinach were operated under good agricultural practice (GAP) in China to human health protective. The dissipation experiments demonstrated that chlorothalonil was rapidly degraded in water spinach, with the half-lives of 1.8-3.2 days, and the amount of its metabolite SDS-3701 (4-hydroxy-2,5,6-trichloroisophthalonitrile) taken up through the water spinach roots from the soil was minor. The terminal experiments disclosed that the average residues of chlorothalonil and SDS-3701 in water spinach were below 6.59 mg/kg and 0.01 mg/kg, respectively. The results suggested the chronic dietary risk probability of chlorothalonil was 51.95-59.15% in terms of all registered crops, and the acute dietary risk probability of chlorothalonil was 12.30%-63.01% in water spinach, highlighting that the dietary risk of chlorothalonil in water spinach under GAP was acceptable. MRL of chlorothalonil was proposed as 7 mg/kg for water spinach and 5 days was recommended as a safe pre-harvest interval (PHI) for chlorothalonil application in water spinach field.