The opportunity to improve the quality of graduate student training for automobile engineering in Chongqing University appears due to the establishment of Chongqing Automotive Collaborative Innovation Center. In this paper, the meaning of collaborative innovation and the drawbacks of professional graduate student training as well as the influence of collaborative innovation on professional graduate student training mode are discussed. The innovation training mode is presented. The multi-disciplinary curriculum system is developed. Practice bases are established and the construction of supervisor team is improved. These explorations and practices provide important references for further deepening the training of professional degree graduate students and improving the level of graduate education.