Schistosomiasis is a water-bourne parasitic disease endemic to Yangtze River basin of China. And the disease epidemic would be seriously influence on the public health and socio-economic developing. After the big flood of 1998, a lot of flood control measures such as “ discharge of flood by removing some of dikes, giving up the cultivated land around for restoreing of lake ' s capacity ” were brought into effect. However, the flood control measures would be extensive in influence on the river ecosystem, and also the Oncomelania snail and Schistosomiasis transmission dynamics was affected by the flood control measures. In this article, the factor that affected transmission dynamics of Oncomelania snail and schistosomiasis was summarized, and the change of Schistosomiasis epidemic after flood control measures implemented was investigated. The results show that: transmission dynamics of Oncomelania snail and schistosomiasis is relation to the nature habitats and human activity, and also relation to the results of interaction between nature habitats and human activity. In the areas where the flood control measures implemented, the transmission dynamics of schistosomiasis present different results because of the different way of the measures implemented. And in this paper the measures controlling epidemic of schistosomiasis were brought forward against the different flood storage and detention areas.