To improve the accuracy and eliminate the error of aircraft assembly, the fixture layout for aircraft frame component with complicated process feature is optimized. In terms of process constraints, a generalized mathematical model of constraints is constructed and a theoretical repairing method is proposed. Additionally, an improved Genetic Algorithm is proposed based on the repairing method. In the example of fixture layout optimization of reconfigurable flexible fixture for frame component, the improved algorithm performed stably and the flexible position error, as a consequence, had reduced dramatically, at around 93.08%. The theoretical analysis and simulation result show that the improved Genetic Algorithm adapts to various kinds of constraint optimization and is feasible for its fast convergence rate and stability.