The uncertain of innovation is increasing under the turbulent environment. The type of innovation is important during the process of innovation practices, but few researches simultaneously consider the factors in the organization effects the choice of the type of innovation. The paper integrates the organization learning theory, the resources based view and the capability based view, analyzes the impacts of cooperative learning on the organization flexibility, on the choice of the type of innovation, and the effects of organization flexibility on choice of the type of innovation.