Aiming at the problems existing in water conservancy and hydro-electric engineering course system in some colleges and universities, such as separation of knowledge structure, some knowledge points repeatedly taught because of the independent knowledge hierarchy separated by courses, as well as contents of teaching materials often lag behind the update of industry standards, in the view of engineering education certification, based on the analysis of the contrary between the current water conservancy and hydro-electric engineering professional course knowledge system and engineering education accreditation, by combing the curriculum system construction ideas of the professional talents training program, the optimization strategy of the curriculum knowledge system adapted to the engineering education certification was proposed, to provide reference for the engineering education certification work of this major.