Today’s market dynamics have made operation process in manufacturing system extremely complex and difficult. Enterprise need to continuous adjust its strategies on evaluating and designing their task and order assignment methods to provide products at the lowest possible cost while reducing the total lead time. The evaluation model based on Holonic Manufacturing System is presented in this paper. The model incorporates operation cost and lead time as the object. A hybrid PSO algorithm with Shuffled Complex Evolution Algorithm(SCE) is utilized to compute the combination optimum for Order assignment problem . Simulation result shows that the model and the algorithm are effective to the problem.