The optimization of complex system is a challenging research field in intelligent optimization. In this paper, the problem of how to decouple the unit of the complex system was proposed. The model on order link settlement in system reconfiguration model based on time Petri-net is put forward, order intelligent operation series is guided by a hybrid particle swarm optimization(HPSO) algorithm with Differential Evolution(DE) algorithm. PSO provides initial solution for DE during the hybrid search process. Such hybrid algorithm can be converted to tradition DE by setting swarm size to one particle. Simulation results show that the proposed model and algorithm are effective to order evaluation and implementation.