With the construction of high dam and large reservoirs, there have been many studies on the impact of flood discharge atomization on the ecological environment, but the impact of flood discharge atomization on pollutant migration and transformation behavior has not attracted attention. In this paper, water samples in multiple sections in front of and below the dam during the flood discharge of the Danjiangkou reservoir in 2019 were collected, the concentrations of 16 polycyclic aromatic hydrocarbons (PAHs) and 6 phthalate acid esters (PAEs) in the water samples were analyzed. It was found that the concentrations of 8 PAHs and 5 PAEs detected in the water below the dam after the flood discharge showed a decreasing trend along the river compared to the section in front of the dam. By comparing the concentration of the section in front of the dam, the concentration reduction ratio of PAHs at 1 km, 5 km and 10 km below the dam was 8.1%-100%, 26.2%-100% and 36.7%-100%, respectively; and the mean values was 34.6%, 64.8% and 75.7%; the concentration reduction ratio of PAEs was 0.9%-38.7%, 33.7%-71.8%, 61.1%-87.5%, respectively; and the average value was 21.5%, 47.0% and 71.3%. Based on the field observation results, the possible migration and transformation pathways and mechanisms of PAHs and PAEs in Danjiangkou Reservoir by dam flood discharge were analyzed. Photodegradation, chemical oxidation, and adsorption of pollutants were considered as the main mechanisms. This study has implications for researching the migration and transformation behaviors of pollutants in water bodies under flood discharge fogging conditions.