The invention relates to an impermeable choking and grouting method for a rock plug truncated cone shell in deepwater, belonging to the method for grouting a rock plug body in deepwater rock plug blasting engineering. The drilling position, drilling interval, drilling direction and drilling depth for grouting can be determined by a group of coaxial truncated cone surface and the cut concentric circle, so that at the periphery of the rock plug and in the rock bodies on the upper opening and the lower opening, compound serum taking cement as base material is filled in cracks and holes of jointsof the rock body, and after the compound serum is cured, the continuously impermeable body with the shape similar to that of the truncated cone shell can be formed in the grouted rock body. In the invention, the purpose is clear and definite, the pertinence is strong, the grouting effect is obvious, the process is clear, and the implementation is simple.