With the continuous expansion of graduate enrollment, local colleges and universities bear the majority of the responsibility for graduate education. Due to geographical and resource limitations, local universities in western China are facing problems such as weak guidance teaching staff, homogeneous competition in disciplines, and insufficient innovation ability of students. To ensure the quality of graduate education is a concern of all sectors of society. In response to the above issues, this article takes the School of Intelligent Technology and Engineering of Chongqing University of Science and Technology as an example to explore the connotation, characteristics, and practical paths of the professional master’s supervisor team cooperation system. By establishing a stable supervisor cooperation model with small teams and large peripherals, the problem of insufficient teaching staff can be addressed. Constructing a 3+2+1 learning time unit and diverse collaborative measures can ensure the cultivation of students’ engineering innovation ability. Creating a 5-dimensional open academic discussion atmosphere to maintain the innovation vitality of teachers and students, promote deep cross integration within the school, between schools, and between schools and enterprises, can alleviate homogeneous competition in disciplines. The collaborative training model of professional master’s supervisors can provide reference for high-quality training of professional master students in other universities in western China.