The rapid changes of market and outer surroundings have caused a dynamic and highly volatile business environment for the enterprise. Manufacturing organizations are seeking efficiency gains by competing via fast time-to-market and low production cost. An Autonomous Agent Network(ANN) Based Manufacturing System model is introduced, as well as the mathematics expression for the components of AAN model. The optimization algorithm based on evolution algorithm is used to solve the optimization problem of the model. Simulation results show that the architecture model and its optimization algorithm are effective to the problem.