To improve the ability of aircraft assembly schedule to deal with unqualified assembly quality，the mapping between assembly quality and quality-related factors and the expression of uncertainty in different decision-making cycles are studied，and the integer programming model is established with the objective function of the scenario-based project expected value. Moreover，based on the trained prediction model of aircraft assembly quality，a multi-layer cyclic iterative search algorithm is designed. The first layer optimizes the execution order of activity based on the activity list coding; The second layer optimizes the personnel allocation through the assembler allocation list; The third layer solves the objective function according to the result of personnel allocation. The numerical results show that the multi-layer cyclic iterative search algorithm can keep the deviation of activity start time below 2 when the predicted workpiece quality is inconsistent with the actual value，which indicates that it is adaptable to the changes of uncertainty factors and can meet the requirements of constructing dynamic schedules for aircraft assembly.