This paper proposes a system, which manages both efficiency and flexiblity ill the AGV (Auto Guided Vehicle) transportation system. Generally, It has been considered that a distributed autonomous system is superior to a centralized system in terms of fail-proof, expansion, load dispersion, flexibility, and the possibility of the evolution. Especially, the most effective characteristic of an autonomous distributed system is a restoration behavior for the system performance. In this paper, to realize the behavior so as to restore the system performance on managing efficiency and flexibility, we propose the method, where each AGV organizes the whole number of the AGV in the system by self-organizing behavior through interaction in the local domain under the change of environment, and evaluate the efficiency which is defined as amount of transportation per an AGV. It is shown that the system exhibits autonomous restoration of the system performance and higher efficiency compared with the centralized system by introducing self-organizing in the dynamical environment.