Aiming at the large-scale complex job-shop scheduling problem of boundary uncertainty and decision preference, a two-stage method which contains interactive scheduling and optimal scheduling is proposed. In the stage of interactive scheduling, a priority rule-based scheduling algorithm which satisfies the multi-constraints is introduced. In the stage of optimal scheduling, the relation between priority rule-based scheduling algorithm and intelligent optimization search method is analyzed, and an intelligent optimization search algorithm combined by priority rule-based scheduling algorithm is designed for optimize the multi-constraints scheduling. The two-stage interactive scheduling method integrates the empirical knowledge and preferences of decision makers, and combines the optimized search algorithm to make the quality of the scheduling solution further improved on the basis of satisfying the decision-maker's preferences. This method has been applied to practical aviation manufacturing factories and gets good effects. Finally, the solution process of an application case is described in detail, and the effectiveness of the proposed method is illustrated