The present application relates to the technical field of water environment governance, and particularly discloses a method for accurate positioning and in-situ treatment of pollutants at a sediment-water interface. In the method, high-throughput sequencing technology and pollutant source apportionment technology are firstly used to perform accurate positioning on the sediment to be controlled, and then electrodialysis-vacuum negative pressure dewatering technology is used to perform in-situ dewatering treatment on the sediment to be controlled, thereby realizing accurate governance with the minimum desilting amount. In the present application, in further cooperation with the application of microbial reagents, the microbial flora environment of the sediment-water interface is regulated, thereby increasing the dewatering speed of the sediment.