Chinese colleges and universities have reached a new stage of development, at which they are shifting from scale expansion to internal quality improvement. So they are clear about their own developing orientation after making their long term planning. The subordinate colleges are the subsidiary units under the universities and directly responsible for achieving the universities’ developing goals; perfecting the management system of subordinate colleges has become the direction of reform of Chinese universities’ administrative management system. The joint conference system between the Party and the administration is the correct choice of the subordinate collage management system along with the tide of historical development; the joint conference system is an organic part of the modern university system with Chinese characteristics, and is the scientific practice to improve the modern university system; the joint conference system can promote democratic management,and is good for the Party to play its role, and is an effective measure to improve the scientific level of the party construction; the joint conference system built the operational mechanism of joint responsibility of Party and administration, and is needed to adapt to situations with Chinese characteristics, and is the inevitable choice of colleges and universities in China. The exploration of the theory and practice of the joint conference system between the Party and the administration of subordinate colleges can provide reference for the deepening of reform of university management system.