The invention discloses hydraulic structure disjoint filling silicone adhesive, which is prepared from a component A and a component B according to a weight proportion, wherein the component A comprises 100 portions of alpha, omega-dihydroxydimethylpolysiloxane and 15 to 45 portions of calcium carbonate filler; and the component B comprises 3 to 10 portions of calcium carbonate filler, 6 to 15 portions of methyl vinyl disilane, and 3 to 10 portions of linear amino polysiloxane cross linker. After stirring and mixing according to the weight proportion, the components are separately sealed and stored; and during use, the component A and the component B are mixed according to the weight proportion and vulcanized at room temperature to form the hydraulic structure disjoint filling silicone adhesive. The hydraulic structure disjoint filling silicone adhesive has the characteristics of room temperature vulcanization, double components, self leveling, adjustable curing speed, low modulus, high elasticity, high durability, free from pollution, free from erosion and the like, belongs to an environment-friendly material, and is mainly used for pouring, filling, sealing and repairing hydraulic structure disjoints of water turbine volutes, water delivery steel pipes and the like.