Abstract: Based on the principle and characteristics of system dynamics, a model was constructed for logistics organization innovation system. The logistic organization system of FT company was simulated with vensim software. The results indicated that the logistic organization innovation system of FT company was an internal innovation development action. It was resulted from the changes of internal and external environment, and was based on logistics resources and logistics capability. It was supported by the organization learning and logistics knowledge, and at the same time, it was also obstructed by cognitive inertia and action inertia of organization.