The invention provides a bottomland ecological interference oncomelania preventing and killing system and method. Multiple separating ditches are arranged according to the water level variation of rivers and lakes, and a high-density oncomelania vegetation region is arranged between the separation ditches. Two separation ditches can be arranged according to the water level of wet season and low-water season; three or more separation ditches can be arranged according to specific condition for a region with complicated water level changes, for example the number of the separation ditches can bearranged according to the water level difference of the wet season water level and the low-water season water level, the number of the separation ditches is in proportional to the water level difference, the number of the separation ditches can be arranged according to the area of the bottomland, and the number of the separation ditches is in proportional to the area; oncomelania blocking nets arearranged in the separation ditches. An oncomelania killing system and method which has a good oncomelania killing effect and small environment influence can be obtained, the system and the method have the advantages of wide application range, large oncomelania treatment area, good oncomelania preventing and killing effect and the like, and the method and the system are suitable for being popularized and used in oncomelania breeding area of bottomlands, dams and the like.