Developing graduate students’ abilities play an important role in the graduate training system. However, training mode with insufficient attention to capability training has some disadvantages, such as course system limitation, simple teaching method and backward evaluation mechanism. It should be reformed to adapt to current society. The capability-oriented graduate training mode has been established with the characteristics of hydraulic structure engineering. According to capability-oriented requirement, graduate student course system is optimized; the participatory teaching mode that suits for the graduate is studied, and the training mechanism to form continuous research capability is presented.