Citrus is the world's largest fruit and an important cash crop in the world. The post-harvest losses of citrus are severe, causing serious economic losses to the citrus industry. In order to reduce the decay of citrus and improve the value of the commodity, Prochloraz and Imazalil are often used in the postharvest handling. In this study, a detection technique of Prochloraz and Imazalil was established based on HPLC. Using this technique, the dynamic of Prochloraz and Imazalil on the postharvest sorting line was detected. It was found that Prochloraz was stable at room temperature, while Imazalil was prone to degrade, and the concentrations of Prochloraz and Imazalil were reduced by 98.6 μg/mL and 290.3 μg/mL, respectively, after 6 h of working on 15 t of Satsuma orange. The results obtained will guide the use of fungicides in the postharvest handling of citrus.