The frequent occurrence of sudden water pollution accidents has become a major threat to water environment safety. Although most researches have focused on constructing 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 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 sudden water accident was predicted through water quality model such as 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 optimize the parameters of soft isolation. Ultimately, the mathematical model of complete purification was formulated in stage 3 to solve 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 sudden water pollution accident in the future.