The basic academic organization is responsible for the research and teaching tasks in universities, which involves teaching reforms and innovations, direct administrations on research and teaching quality, as well as managements of student’s daily life This paper defined the basic academic organization and pointed out its micro behavior modes and its theory We think, based on efficiency and integration, college is supposed to be the form of the basic organization which represents in different ways, such as academic leadership systems, task research centers, temporary research teams, research and teaching centers across subjects and colleges,dean’s joint meetings and etc The functions and results are limited by the perfection of the system, which includes the confirmation of qualification and ability, the responsibility of chief professor, the achievement and evaluation standard, as well as the sources of the evaluation information and the establishment of incentive systems Key words： university; basic academic organization; innovation system