With the development of economy and society, new and higher demands on innovation team construction of civil subject are needed in applicationoriented institutes. To improve the existing organization mode of innovation team, make the subject orientation relatively centralized and stable, optimize the subject structure, and achieve aims of cultivating applied talents to serve the society, it is necessary to build a new organization mode. In the construction process, team goals, scientific research groups, resources assessment system, and incentive mechanism are four basic elements. To construct a continuously mature and improved dynamic organization mode, they must be combined organically by doing a series of activities, including determining research goals, selecting members, allocating roles, establishing a scientific research echelon, and solving critical projects.