Objective To analyze and evaluate the related data of bottom clearance in Fuling section of Three Gorges Reservoir. Methods Bottom clearance in Fuling section of Three Gorges Reservoir was carried out in Fuling district during the period from May to December in 2002. All the data related to clearance were collected before and after the bottom clearance. Based on the collected data, the effect of clearance was assessed. Results 5 882 general pollution sources, 68 contagion pollution sources were cleaned in Fuling district, the clearance rates of both were 100%. The rat densities in agriculture areas and the dismantling cities were 3.97% and 2.97% respectively before rat extinguishment, then became 0.65% and 0.33% after rat extinguishment. Conclusion Through the bottom clearance of Three Gorges Reservoir, contagion and general pollution sources in the emigrant areas have been cleaned up, so water pollution in Three Gorges Reservoir and the rats mediated diseases have been prevented and controlled.