A mathematical model was constructed with two objectives. A two-stage hybrid algorithm was developed for solving this problem. At first, the man-hour optimization based on genetic algorithm and dynamic programming method, the model decomposes the flow shop into two layers: sub-layer and patrilineal layer. On the basis of the man-hour optimization，A simulated annealing genetic algorithm was proposed to optimize the sequence of operations. A new selection procedure was proposed and hybrid crossover operators and mutation operators were adopted. A benchmark problem solving result indicates that the proposed algorithm is effective.