In view of the characteristic that multi-objective optimization algorithms are sensitive to objective order, objective order sensitivity analysis based on grey and entropy parallel analysis is proposed. Taking multi-objective flow shop scheduling problem as object, flow shop scheduling model of different objective order is established, and GA based on grey and entropy parallel analysis is used to optimize the multi-objective model of different objective order. Then sensitive coefficient is defined and graphics of sensitive coefficient is drew. The experiment results show that grey and entropy parallel analysis is sensitive to objective order, ascending and descending order ordered by the size of objective value are not the best, and sensitive coefficient of shock order is the smallest. It indicates that we should select reasonable objective order to get better optimization results for multi-objective optimization. Also algorithm fitness value is sensitive to objective order, which effects significantly on the algorithm performance.