The Three Gorges Reservoir (TGR) is totally manmade, strongly influenced by anthropogenic activity, and lies on the upper reaches of Yangtze River. The periodic storage and discharge of water from the Three Gorges Dam could have altered the original air-plant/soil interactions of contaminants in TGR. Herein, paired atmospheric gas–particle, air–plant, and air–soil samples were collected to investigate the air–plant interaction and air–soil exchange of 16 USEPA priority polycyclic aromatic hydrocarbons (PAHs). The air–plant interaction based on McLachlan's framework to our datasets suggests that PAHs were absorbed via gaseous deposition that was restricted by the plant–gas dynamic equilibrium. The equilibrium indicates a dynamic balance between the gaseous phase and plant surface in PAH absorption. The main limiting factor influencing the PAH uptake was the plant species rather than the atmospheric PAH concentration. The air–soil exchange of PAHs exhibited a net volatilization flux of 16.71 ng/m2/d from the soil to the air based on annual average. There was more volatilization and less deposition in summer and more deposition and less volatilization in autumn and winter. The soil serves as a secondary source of atmospheric PAHs. As the first attempt on probing the multi-interface geochemical process of PAHs, this study highlights the influence of manual water level manipulation from the TGD and environmental factors (such as temperature, humidity, and soil properties) on the regional fate of PAHs in the TGR.