In order to effectively plug the fracture channeling-path in the high water cut fractured low permeability reservoir, a new type of water shutoff agent is developed by bottle tests and its injectivity and plugging performance in fractures are systematically studied by rheology and fractured core displacement experiment. The gelant consists of modified starch, dimethyl diallyl ammonium chloride, N,N′-methylene diacrylamide, and potassium persulfate, which behaves as a Newtonian with a good flowing capacity that allows its accurate positioning in the fractures. After gelatinization, the gel has high elastic modulus and viscous modulus. During the gelant injection into the fractured core, the filtration from fracture into matrix of the gelant leads to a difference between the injection volume of the gelant and the plugged fracture volume. Thus, a mathematical model for calculating filtration volume is established and applied in plugging experiment very well. After plugging, the two block cores can be tightly cemented together by the starch gel. The experiments show that the water shutoff agent and the mathematical model of filtration can be used to effectively plug the fracture channeling-path in the high water cut fractured low permeability reservoir.