Through the characteristics of engineering management specialty, the paper analyzed the main problems in the present graduation design mode of application-oriented universities,put forward a “group” guidance mode with multi-disciplinary penetration, multi-disciplinary cross, combination of inside and outside of the school and integration two stages of the ability. This mode will affect graduation design result in engineering management specialty of application-oriented universities, it is a new way to show the exploration and practice of graduation design in engineering management specialty.