Optimal coordination is essential for multi‐automated guided vehicle (AGV) systems, particularly in logistic transportation cases, where the system task completion time needs to be minimized, with the guarantee of safe operation. This is because an optimal coordination strategy (OCS), if achieved, can significantly improve the transportation system's efficiency. In this paper, to deal with the dynamic interaction process among AGVs, and sensing and communication range limits, we formulate the optimal coordination problem into a distributed differential game (DDG) framework, where individual AGVs only use information communicated from nearby AGVs to design their optimal operation trajectories. This helps to significantly reduce the computational and communication requirements for the multi‐AGV logistic transportation systems. Targeting operation safety and working efficiency requirements, we incorporate collision avoidance and trajectory optimization objectives into the proposed framework. It is shown that local OCS, obtained by solving the DDG problem for each AGV, will converge to the global Nash equilibrium, which represents the most efficient operating condition for the entire logistic transportation system. Finally, the efficacy of the proposed method is demonstrated, based on simulations and experiments, benchmarked with existing logistic warehousing planning and differential game methods. Compared with conventional methods, the proposed framework successfully helps reduce the task completion time by up to 16%.