A growing number of colleges and universities inherit the spirit and tradition of Chinese ancient academy, draw lessons from western boarding experience, explore the training mode of college system according with the spirit of the times in order to promote the teaching reform of higher education. On the basis of the growth of students,the successful experience of higher education reform at home and abroad, an idea of college system reform is graduatly formed in Nanjing Audit University. Following the modern higher education rules, this paper puts forward the talent training innovation system in command of whole person education philosophy, with the collaboration of two mechanisms (the Institute, the Academy), optimization of three-whole modes ( whole staff education, whole process of education and all-round education), linkage of four factors ( general education, tutorial system, credit system and boarding system) and the integration of five systems ( talent training system, academic counseling system, comprehensive quality promotion system, independent management system and “three service linkage” support system ).