The invention discloses a water proofing method for the situation that a pipeline penetrates a hydraulic structure settlement joint. The water proofing method comprises the specific steps that a rigid waterproof casing pipe and the rigid wall penetrating pipeline are mounted, and the casing pipe and the pipeline are filled with batched jute and asbestos cement. According to the water proofing method, the rigid-flexible combined connection manner is adopted, the water proofing purpose of the portion between the wall penetrating pipeline and a penetrated wall body is achieved, and destruction to the structure due to uneven settlement is eliminated as well. The water proofing method has the beneficial effects of being good in water proofing effect, convenient to construct and maintain, high in applicability and the like.