Under the background of emerging engineering education, the cultivation of outstanding scientific and technological talents in geotechnical engineering asks for higher requirements for graduate education in terms of innovation, scientific research and academy. "Scientific scaffolding" mode recommended by this research is created under "capability domain" for the first time, which is different from the traditional teaching mode, and designed by considering competency training rather than contents of courses. The graduate education is a process of construction of ability system, namely, the building of "scientific scaffolding". In the training programs, curriculum teaching is the initial period and critical part for the assembling of "scientific scaffolding", which is given by distinct researching attributes. Courses organized within multi-disciplines, are taught by learning a series of special subjects, forming a new education pattern that learning a special subject, carrying out a research at the same time. The training of scientific research is conducted through the whole process of graduate education from the beginning. In this paper, the theoretical basis of "scientific scaffolding" mode is discussed, the designing idea is presented, the implementation processes are investigated, and ideal teaching effects are highlighted in practice, which may break new frontiers for the graduate education.