Abstract: With the technological development of manufacturing industry, the requirement of customer is moving toward diversity, small-scale, or even single-piece production. Customized production is mainly suitable for the aircraft and ship manufacturing industry. Conversely, the production method oriented to whole-set orders is having a more and more wide applications. However, up to now, there have been few related works on this issue of whole-set orders, due to the special nature of the flexible job shop and the complexity of the whole-set orders scheduling. To this end, this paper proposes a new scheduling model under flexible job shop environment so as to maximize the whole-set ratio of weighted orders. Meanwhile, the three distinctive characteristics are analyzed. In order to find the global optimal solution, a new neighborhood structure is proposed according to the characteristics of the whole-set orders scheduling model. A novel max-min ant algorithm with a neighborhood structure (MMAS-NS) is constructed based on the basic max-min ant system (MMAS), which can improve the objective by reducing and eliminating bottlenecks of delivery time for orders and workpieces. The influence of each parameter on the performance of algorithms is analyzed by orthogonal experiments, which also verifies the effectiveness of new neighborhood structure. Finally, the comparison with other novel meta-heuristic algorithms, e.g., imperialist competitive algorithm, is made, from which it is shown that the proposed MMAS-NS algorithm can effectively improve the whole-set ratio of weighted order.