Graduation design is an important stage of undergraduate teaching. There are some difficulties in the organization of graduation design in independent colleges. A series of exploration and innovation were carried out in the department of civil engineering, Zhicheng College, Fuzhou University, including overall arrangement beforehand, group setting according to employment trends of graduations, close cooperation with enterprises and professional experts in the whole process, selecting topics according to engineering practice, effective process control measures, and improvement in grade evaluation methods. The results show that the teaching reform and practice are effective to solve the problems existing in the graduation design process in independent colleges and important in improving education quality and promoting graduation employment.