Considering the background of cloud manufacturing and cluster supply chain, we build the basic model to assign the orders priority within each capacity. Then, considering the inter-chain horizontal cooperation, the extended model is proposed to parallel allocation of cross-chain orders as the orders exceeding one single- chain’s capacity. Lagrange algorithm is implemented, and the simulation analysis shown that the opportunity cost of rejected orders factor and cross-chain orders manufacturing cost factor have significant impacts on orders’ allocation decision, and there is a critical point in the combinations of those two factors. Through combinations, the cluster supply chain can make the acceptance decisions policy and production schedules of priority orders and cross- chain orders, so that customers’ satisfaction and the cluster supply chain’s total profits achieve the best situations.