with the tendency of economic globalization, industrialization, informatization and the requirement of developing domestic economy, building innovative country, the social demand of applied engineering intelligentsia is increasingly enhancing. On the basis of engineering master & doctor’s cultivation practice of Tokyo Tech, Tohoku University and Kyoto University, this paper expounds their educational modes’ characteristic, development and reformation, and accordingly refines the feature and experience of cultivation modes’ innovation in higher engineering education at Japan’s national universities, thus providing significant implication for the current practice of engineering master & doctor’s implement in our country.