In order to solve the flow shop multi-objective scheduling optimization problem and the algorithm fitness value assignment problem, the distribution strategy of the grey entropy relational adaptive value is proposed combined with grey correlation analysis method and the theory of the information entropy, and the fitness value is calculated combined with the grey correlation and entropy weight coefficient. The grey entropy correlation grade is used to guide the evolution of the heuristic algorithm. This method is introduced to the difference algorithm and the genetic algorithm to solve three objective flow shop scheduling problem. The experimental results show that grey entropy relational adaptive value allocation strategies can solve this problem effectively, and can get uniform distribution of the Pareto front. Meanwhile, the difference algorithm based on this strategy can abtain better solutions than the genetic algorithm.