In this study, a coupled Weather Research and Forecasting-Community Multiscale Air Quality (WRF-CMAQ) model was developed to analyze the atmospheric transport of polychlorinated dibenzo-p-dioxins and furans (PCDD/Fs) in the megacity of Shanghai, and the population’s exposure to them. The results showed that 69.88% of the simulated values are within 0.5 to 2 times the observed values, indicating good accuracy. In 2019, the highest PCDD/Fs pollution levels in Shanghai’s atmosphere were observed in winter, followed by fall and spring. The lowest levels occurred in summer, with respective mass concentrations of 847.08, 629.53, 588.38, and 406.96 fg/m3 and respective TEQ concentrations of 59.29, 44.46, 40.80, and 28.08 fg I-TEQ/m3. The areas most polluted with atmospheric PCDD/Fs were Yangzi, Yangzhou, and Shanghai. Fs were found in Yangpu, Hongkou, Huangpu, Jing'an, Baoshan, Jinshan, and Songjiang. The respiratory exposure of Shanghai residents to PCDD/Fs followed the trend of adolescents > elderly > middle-aged people, with 10.67, 8.86, and 8.47 fg I-TEQ/(kg·d), and the risk of exposure was within the acceptable range. The contribution of local emission sources is much larger than that of foreign emission sources, indicating that local industrial production processes and combustion activities mainly cause atmospheric PCDD/Fs pollution in Shanghai.