The frequent occurrence of sudden water pollution accidents has become a major threat to water environment safety. Although most researches have focused on constructing a pollutant source identification model and risk assessment methods for dealing with sudden water pollution accidents, a real-time, effective emergency measure for controlling pollutant diffusion, isolating and removing the pollutant, aiming at sudden water pollution accidents, has not been emphasized. Therefore, in this paper, a novel emergency approach of soft isolation was investigated to control pollution diffusion and decrease damage as soon as the accident occurred. In stage 1, the feature of pollution diffusion regarding a sudden water accident was predicted through a water quality model using computational fluid dynamics (CFD). Then, a design scheme of soft isolation was constructed in stage 2 to isolate the polluted zone and attention was paid to optimizing the parameters of soft isolation. Ultimately, the mathematical model of complete purification was formulated in stage 3 to remove the pollution from the impacted zone. The results indicated that the emergency measure of soft isolation could have significant potential to control and isolate pollution occurring in a sudden water pollution accident in the future.